Code
library(knitr)
library(targets)
library(MiscMetabar)
library(patchwork)
here::i_am("analysis/01_bioinformatics.qmd")
source(here::here("R/styles.R"))
source(here::here("R/functions.R"))Where we see the pipeline processes
Date: December 3, 2024
library(knitr)
library(targets)
library(MiscMetabar)
library(patchwork)
here::i_am("analysis/01_bioinformatics.qmd")
source(here::here("R/styles.R"))
source(here::here("R/functions.R"))conflicted::conflicts_prefer(dplyr::filter)[conflicted] Will prefer dplyr::filter over any other package.
conflicted::conflicts_prefer(dplyr::rename)[conflicted] Will prefer dplyr::rename over any other package.
res_ga <- greenAlgoR::ga_targets(store = here::here("_targets/"))
library("emojifont")
ggvalue_box(
round(res_ga$carbon_footprint_total_gCO2),
"Carbon footprint (g)",
icons = fontawesome(search_fontawesome("industry")[1]),
alpha_icon = 0.7,
colors = idest_pal$ligth_color_idest[[1]][[3]],
color_icon = idest_pal$dark_color_idest[[1]][[5]],
value_font_color = idest_pal$dark_color_idest[[1]][[5]],
lab_font_color = idest_pal$dark_color_idest[[1]][[5]]
) +
ggvalue_box(
round(res_ga$energy_needed_kWh, 2),
"Energy used (kWh)",
icons = fontawesome(search_fontawesome("bolt")),
alpha_icon = 0.7,
colors = idest_pal$ligth_color_idest[[1]][[1]],
color_icon = idest_pal$dark_color_idest[[1]][[2]],
value_font_color = idest_pal$dark_color_idest[[1]][[2]],
lab_font_color = idest_pal$dark_color_idest[[1]][[2]]
)log_data <- autometric::log_read(
here::here("data/data_final/autometric_log.txt"),
units_time = "hours",
units_memory = "gigabytes"
)
res <- NULL
for(pid_char in as.character(rev(unique(log_data$pid)))) {
print(pid_char)
print(paste0("NROW=", nrow(res)))
for (phase_char in unique(log_data$phase)) {
print(phase_char)
if (sum(res$phase == phase_char) == 0) {
ld <- log_data |>
filter(phase == phase_char) |>
filter(pid == pid_char)
print(paste0("nrow_ld:",nrow(ld)))
res <- bind_rows(ld, res)
} else {
print(paste0("nrow=", nrow(res)))
}
}
}[1] "10720"
[1] "NROW="
[1] "__DEFAULT__"
[1] "nrow_ld:12"
[1] "cutadapt"
[1] "nrow_ld:0"
[1] "quality_seq_wo_primers"
[1] "nrow_ld:0"
[1] "filtered"
[1] "nrow_ld:0"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow_ld:0"
[1] "conclude: derep_fs"
[1] "nrow_ld:0"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow_ld:0"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow_ld:0"
[1] "derep_rs"
[1] "nrow_ld:0"
[1] "conclude: derep_rs"
[1] "nrow_ld:0"
[1] "err_fs"
[1] "nrow_ld:0"
[1] "err_rs"
[1] "nrow_ld:0"
[1] "ddF"
[1] "nrow_ld:0"
[1] "conclude: ddF"
[1] "nrow_ld:0"
[1] "ddR"
[1] "nrow_ld:0"
[1] "conclude: ddR"
[1] "nrow_ld:0"
[1] "merged_seq"
[1] "nrow_ld:0"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "seqtab_wo_chimera"
[1] "nrow_ld:0"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow_ld:0"
[1] "tax_tab"
[1] "nrow_ld:0"
[1] "conclude: tax_tab"
[1] "nrow_ld:0"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow_ld:0"
[1] "d_vs"
[1] "nrow_ld:0"
[1] "d_vs_mumu"
[1] "nrow_ld:0"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow_ld:0"
[1] "bioinfo_report"
[1] "nrow_ld:68"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "fastq_files_folder"
[1] "nrow_ld:0"
[1] "quality_raw_seq"
[1] "nrow_ld:0"
[1] "data_phyloseq"
[1] "nrow_ld:0"
[1] "conclude: d_vs"
[1] "nrow_ld:0"
[1] "d_vs_mumu_rarefy"
[1] "nrow_ld:0"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow_ld:0"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "150107"
[1] "NROW=80"
[1] "__DEFAULT__"
[1] "nrow=80"
[1] "cutadapt"
[1] "nrow_ld:0"
[1] "quality_seq_wo_primers"
[1] "nrow_ld:0"
[1] "filtered"
[1] "nrow_ld:0"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow_ld:0"
[1] "conclude: derep_fs"
[1] "nrow_ld:0"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow_ld:0"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow_ld:0"
[1] "derep_rs"
[1] "nrow_ld:0"
[1] "conclude: derep_rs"
[1] "nrow_ld:0"
[1] "err_fs"
[1] "nrow_ld:0"
[1] "err_rs"
[1] "nrow_ld:0"
[1] "ddF"
[1] "nrow_ld:0"
[1] "conclude: ddF"
[1] "nrow_ld:0"
[1] "ddR"
[1] "nrow_ld:0"
[1] "conclude: ddR"
[1] "nrow_ld:0"
[1] "merged_seq"
[1] "nrow_ld:0"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "seqtab_wo_chimera"
[1] "nrow_ld:0"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow_ld:0"
[1] "tax_tab"
[1] "nrow_ld:0"
[1] "conclude: tax_tab"
[1] "nrow_ld:0"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow_ld:0"
[1] "d_vs"
[1] "nrow_ld:0"
[1] "d_vs_mumu"
[1] "nrow_ld:0"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow_ld:0"
[1] "bioinfo_report"
[1] "nrow=80"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "fastq_files_folder"
[1] "nrow_ld:0"
[1] "quality_raw_seq"
[1] "nrow_ld:0"
[1] "data_phyloseq"
[1] "nrow_ld:0"
[1] "conclude: d_vs"
[1] "nrow_ld:0"
[1] "d_vs_mumu_rarefy"
[1] "nrow_ld:0"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow_ld:0"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "77376"
[1] "NROW=80"
[1] "__DEFAULT__"
[1] "nrow=80"
[1] "cutadapt"
[1] "nrow_ld:350"
[1] "quality_seq_wo_primers"
[1] "nrow_ld:498"
[1] "filtered"
[1] "nrow_ld:509"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow_ld:160"
[1] "conclude: derep_fs"
[1] "nrow_ld:30"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow_ld:242"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow_ld:242"
[1] "derep_rs"
[1] "nrow_ld:173"
[1] "conclude: derep_rs"
[1] "nrow_ld:50"
[1] "err_fs"
[1] "nrow_ld:78"
[1] "err_rs"
[1] "nrow_ld:138"
[1] "ddF"
[1] "nrow_ld:1070"
[1] "conclude: ddF"
[1] "nrow_ld:2"
[1] "ddR"
[1] "nrow_ld:1195"
[1] "conclude: ddR"
[1] "nrow_ld:2"
[1] "merged_seq"
[1] "nrow_ld:117"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow_ld:1"
[1] "seqtab_wo_chimera"
[1] "nrow_ld:25"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow_ld:1"
[1] "tax_tab"
[1] "nrow_ld:8945"
[1] "conclude: tax_tab"
[1] "nrow_ld:1"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow_ld:6549"
[1] "d_vs"
[1] "nrow_ld:8"
[1] "d_vs_mumu"
[1] "nrow_ld:6"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow_ld:131"
[1] "bioinfo_report"
[1] "nrow=20603"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "track_sequences_samples_clusters"
[1] "nrow_ld:97"
[1] "fastq_files_folder"
[1] "nrow_ld:5"
[1] "quality_raw_seq"
[1] "nrow_ld:525"
[1] "data_phyloseq"
[1] "nrow_ld:1"
[1] "conclude: d_vs"
[1] "nrow_ld:1"
[1] "d_vs_mumu_rarefy"
[1] "nrow_ld:1"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow_ld:1"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow_ld:1"
[1] "90857"
[1] "NROW=21235"
[1] "__DEFAULT__"
[1] "nrow=21235"
[1] "cutadapt"
[1] "nrow=21235"
[1] "quality_seq_wo_primers"
[1] "nrow=21235"
[1] "filtered"
[1] "nrow=21235"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow=21235"
[1] "conclude: derep_fs"
[1] "nrow=21235"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow=21235"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow=21235"
[1] "derep_rs"
[1] "nrow=21235"
[1] "conclude: derep_rs"
[1] "nrow=21235"
[1] "err_fs"
[1] "nrow=21235"
[1] "err_rs"
[1] "nrow=21235"
[1] "ddF"
[1] "nrow=21235"
[1] "conclude: ddF"
[1] "nrow=21235"
[1] "ddR"
[1] "nrow=21235"
[1] "conclude: ddR"
[1] "nrow=21235"
[1] "merged_seq"
[1] "nrow=21235"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow=21235"
[1] "seqtab_wo_chimera"
[1] "nrow=21235"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow=21235"
[1] "tax_tab"
[1] "nrow=21235"
[1] "conclude: tax_tab"
[1] "nrow=21235"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow=21235"
[1] "d_vs"
[1] "nrow=21235"
[1] "d_vs_mumu"
[1] "nrow=21235"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow=21235"
[1] "bioinfo_report"
[1] "nrow=21235"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow_ld:4"
[1] "track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "fastq_files_folder"
[1] "nrow=21239"
[1] "quality_raw_seq"
[1] "nrow=21239"
[1] "data_phyloseq"
[1] "nrow=21239"
[1] "conclude: d_vs"
[1] "nrow=21239"
[1] "d_vs_mumu_rarefy"
[1] "nrow=21239"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow=21239"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "75659"
[1] "NROW=21239"
[1] "__DEFAULT__"
[1] "nrow=21239"
[1] "cutadapt"
[1] "nrow=21239"
[1] "quality_seq_wo_primers"
[1] "nrow=21239"
[1] "filtered"
[1] "nrow=21239"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow=21239"
[1] "conclude: derep_fs"
[1] "nrow=21239"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow=21239"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow=21239"
[1] "derep_rs"
[1] "nrow=21239"
[1] "conclude: derep_rs"
[1] "nrow=21239"
[1] "err_fs"
[1] "nrow=21239"
[1] "err_rs"
[1] "nrow=21239"
[1] "ddF"
[1] "nrow=21239"
[1] "conclude: ddF"
[1] "nrow=21239"
[1] "ddR"
[1] "nrow=21239"
[1] "conclude: ddR"
[1] "nrow=21239"
[1] "merged_seq"
[1] "nrow=21239"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow=21239"
[1] "seqtab_wo_chimera"
[1] "nrow=21239"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow=21239"
[1] "tax_tab"
[1] "nrow=21239"
[1] "conclude: tax_tab"
[1] "nrow=21239"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow=21239"
[1] "d_vs"
[1] "nrow=21239"
[1] "d_vs_mumu"
[1] "nrow=21239"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow=21239"
[1] "bioinfo_report"
[1] "nrow=21239"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "fastq_files_folder"
[1] "nrow=21239"
[1] "quality_raw_seq"
[1] "nrow=21239"
[1] "data_phyloseq"
[1] "nrow=21239"
[1] "conclude: d_vs"
[1] "nrow=21239"
[1] "d_vs_mumu_rarefy"
[1] "nrow=21239"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow=21239"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "170193"
[1] "NROW=21239"
[1] "__DEFAULT__"
[1] "nrow=21239"
[1] "cutadapt"
[1] "nrow=21239"
[1] "quality_seq_wo_primers"
[1] "nrow=21239"
[1] "filtered"
[1] "nrow=21239"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow=21239"
[1] "conclude: derep_fs"
[1] "nrow=21239"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow=21239"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow=21239"
[1] "derep_rs"
[1] "nrow=21239"
[1] "conclude: derep_rs"
[1] "nrow=21239"
[1] "err_fs"
[1] "nrow=21239"
[1] "err_rs"
[1] "nrow=21239"
[1] "ddF"
[1] "nrow=21239"
[1] "conclude: ddF"
[1] "nrow=21239"
[1] "ddR"
[1] "nrow=21239"
[1] "conclude: ddR"
[1] "nrow=21239"
[1] "merged_seq"
[1] "nrow=21239"
[1] "seq_tab_Pairs"
[1] "nrow_ld:1"
[1] "conclude: seq_tab_Pairs"
[1] "nrow=21240"
[1] "seqtab_wo_chimera"
[1] "nrow=21240"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow=21240"
[1] "tax_tab"
[1] "nrow=21240"
[1] "conclude: tax_tab"
[1] "nrow=21240"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:1"
[1] "d_asv"
[1] "nrow=21241"
[1] "d_vs"
[1] "nrow=21241"
[1] "d_vs_mumu"
[1] "nrow=21241"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:1"
[1] "track_by_samples"
[1] "nrow=21242"
[1] "bioinfo_report"
[1] "nrow=21242"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow=21242"
[1] "track_sequences_samples_clusters"
[1] "nrow=21242"
[1] "fastq_files_folder"
[1] "nrow=21242"
[1] "quality_raw_seq"
[1] "nrow=21242"
[1] "data_phyloseq"
[1] "nrow=21242"
[1] "conclude: d_vs"
[1] "nrow=21242"
[1] "d_vs_mumu_rarefy"
[1] "nrow=21242"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow=21242"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow=21242"
[1] "145218"
[1] "NROW=21242"
[1] "__DEFAULT__"
[1] "nrow=21242"
[1] "cutadapt"
[1] "nrow=21242"
[1] "quality_seq_wo_primers"
[1] "nrow=21242"
[1] "filtered"
[1] "nrow=21242"
[1] "prepare: derep_fs"
[1] "nrow_ld:1"
[1] "derep_fs"
[1] "nrow=21243"
[1] "conclude: derep_fs"
[1] "nrow=21243"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow=21243"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow=21243"
[1] "derep_rs"
[1] "nrow=21243"
[1] "conclude: derep_rs"
[1] "nrow=21243"
[1] "err_fs"
[1] "nrow=21243"
[1] "err_rs"
[1] "nrow=21243"
[1] "ddF"
[1] "nrow=21243"
[1] "conclude: ddF"
[1] "nrow=21243"
[1] "ddR"
[1] "nrow=21243"
[1] "conclude: ddR"
[1] "nrow=21243"
[1] "merged_seq"
[1] "nrow=21243"
[1] "seq_tab_Pairs"
[1] "nrow=21243"
[1] "conclude: seq_tab_Pairs"
[1] "nrow=21243"
[1] "seqtab_wo_chimera"
[1] "nrow=21243"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow=21243"
[1] "tax_tab"
[1] "nrow=21243"
[1] "conclude: tax_tab"
[1] "nrow=21243"
[1] "conclude: data_phyloseq"
[1] "nrow=21243"
[1] "d_asv"
[1] "nrow=21243"
[1] "d_vs"
[1] "nrow=21243"
[1] "d_vs_mumu"
[1] "nrow=21243"
[1] "conclude: d_vs_mumu"
[1] "nrow=21243"
[1] "track_by_samples"
[1] "nrow=21243"
[1] "bioinfo_report"
[1] "nrow=21243"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow=21243"
[1] "track_sequences_samples_clusters"
[1] "nrow=21243"
[1] "fastq_files_folder"
[1] "nrow=21243"
[1] "quality_raw_seq"
[1] "nrow=21243"
[1] "data_phyloseq"
[1] "nrow=21243"
[1] "conclude: d_vs"
[1] "nrow=21243"
[1] "d_vs_mumu_rarefy"
[1] "nrow=21243"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow=21243"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow=21243"
autom_p <- res |>
filter(!grepl("conclude:", phase)) |>
filter(!grepl("prepare:", phase)) |>
filter(!grepl("__DEFAULT__", phase)) |>
ggplot(aes(x = time, y = reorder(phase, dplyr::desc(time)), color = resident)) +
geom_line(aes(linewidth = cpu)) +
scale_color_viridis_b("Memory (Gb)", end = 0.9, direction = -1) +
theme_idest() +
xlab("Time (in hours)") +
ylab("Targets")
autom_p + xlim(c(167, 174))data_2 <- autom_p$data |>
group_by(phase) |>
summarise(time=min(time), resident = mean(resident))
autom_p + geom_point(data = data_2, shape=3) + xlim(c(167, 174))d_pq <- clean_pq(tar_read("d_vs", store = here::here("_targets/")))Cleaning suppress 2 taxa and 12 samples.
summary_plot_pq(d_pq)Cleaning suppress 0 taxa and 0 samples.
tar_glimpse(script = here::here("_targets.R"),
targets_only = TRUE,
callr_arguments = list(show = FALSE))tar_meta(store = here::here("_targets/"), targets_only = TRUE) |>
dplyr::mutate(time = paste0(seconds %/% 3600, ":", seconds %/% 60, ":", floor(seconds %% 60))) |>
dplyr::select(name, seconds, bytes, format, time) |>
dplyr::mutate(Gb = round(bytes / 10^9, 2)) |>
dplyr::arrange(desc(seconds), desc(bytes)) |>
kable()| name | seconds | bytes | format | time | Gb |
|---|---|---|---|---|---|
| tax_tab | 8950.164 | 1291675 | rds | 2:149:10 | 0.00 |
| d_asv | 6549.617 | 1750186 | rds | 1:109:9 | 0.00 |
| ddR | 1195.932 | 119142011 | qs | 0:19:55 | 0.12 |
| ddF | 1070.724 | 105563116 | qs | 0:17:50 | 0.11 |
| quality_raw_seq | 524.808 | 18320 | rds | 0:8:44 | 0.00 |
| filtered | 509.565 | 182 | rds | 0:8:29 | 0.00 |
| quality_seq_wo_primers | 497.925 | 18660 | rds | 0:8:17 | 0.00 |
| cutadapt | 349.122 | 86016 | file | 0:5:49 | 0.00 |
| quality_seq_filtered_trimmed_FW | 240.991 | 11385 | rds | 0:4:0 | 0.00 |
| quality_seq_filtered_trimmed_REV | 240.823 | 11385 | rds | 0:4:0 | 0.00 |
| derep_rs | 173.771 | 1932493611 | qs | 0:2:53 | 1.93 |
| derep_fs | 159.974 | 1102690227 | qs | 0:2:39 | 1.10 |
| err_rs | 137.626 | 24539 | qs | 0:2:17 | 0.00 |
| track_by_samples | 131.940 | 9193 | rds | 0:2:11 | 0.00 |
| merged_seq | 116.616 | 2140786 | qs | 0:1:56 | 0.00 |
| track_sequences_samples_clusters | 97.023 | 444 | rds | 0:1:37 | 0.00 |
| err_fs | 77.500 | 20518 | qs | 0:1:17 | 0.00 |
| bioinfo_report | 67.736 | 44 | rds | 0:1:7 | 0.00 |
| seqtab_wo_chimera | 25.524 | 1287050 | rds | 0:0:25 | 0.00 |
| d_vs | 7.971 | 1421936 | rds | 0:0:7 | 0.00 |
| d_vs_mumu | 5.892 | 1393310 | rds | 0:0:5 | 0.00 |
| d_vs_mumu_rarefy | 0.872 | 1326445 | rds | 0:0:0 | 0.00 |
| data_phyloseq | 0.587 | 1619162 | rds | 0:0:0 | 0.00 |
| seq_tab_Pairs | 0.302 | 1595472 | rds | 0:0:0 | 0.00 |
| s_d | 0.046 | 10962 | rds | 0:0:0 | 0.00 |
| asv_tab | 0.040 | 1272832 | rds | 0:0:0 | 0.00 |
| seqtab | 0.025 | 1272901 | rds | 0:0:0 | 0.00 |
| data_raw | 0.021 | 5385 | rds | 0:0:0 | 0.00 |
| sam_tab | 0.003 | 3608 | rds | 0:0:0 | 0.00 |
| file_sam_data_csv | 0.001 | 7392 | file | 0:0:0 | 0.00 |
| file_refseq_taxo | 0.000 | 114270891 | file | 0:0:0 | 0.11 |
| fastq_files_folder | 0.000 | 49152 | file | 0:0:0 | 0.00 |
| data_fnfs | 0.000 | 2792 | rds | 0:0:0 | 0.00 |
| data_fnrs | 0.000 | 2791 | rds | 0:0:0 | 0.00 |
| samp_n_otu_table | 0.000 | 1848 | rds | 0:0:0 | 0.00 |
d_pq <- tar_read("d_vs", store = here::here("_targets/"))The {targets} package is at the core of this project. Please read the intro of the user manual if you don’t know {targets}.
The {targets} package store … targets in a folder and can load (tar_load()) and read (tar_read) object from this folder.
DT::datatable(d_pq@sam_data)kable(tar_read(track_sequences_samples_clusters, store = here::here("_targets/")))| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| Raw Forward sequences | 19954015 | NA | 371 |
| Forward wo primers | 18017803 | NA | 371 |
| Forward sequences | 14870347 | 31999 | 352 |
| Paired sequences | 13348696 | 21262 | 352 |
| Paired sequences without chimera | 12747603 | 16531 | 352 |
| Paired sequences without chimera and longer than 200bp | 12656354 | 15832 | 352 |
| ASV denoising | 12523823 | 15832 | 351 |
| OTU after vsearch reclustering at 97% | 12523823 | 6679 | 351 |
| OTU vs after mumu cleaning algorithm | 12523823 | 5896 | 339 |
| OTU vs + mumu + rarefaction by sequencing depth | 644000 | 4567 | 322 |
tab_samp <- tar_read(track_by_samples, store = here::here("_targets/"))
for (li in names(tab_samp)) {
print(knitr::kable(tab_samp[[li]], caption = li, format = "html"))
cat("\n<!-- -->\n\n")
}| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 36227 | 37 | 1 |
| OTU after vsearch reclustering at 97% | 36227 | 29 | 1 |
| OTU vs after mumu cleaning algorithm | 36227 | 24 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 22 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 39120 | 159 | 1 |
| OTU after vsearch reclustering at 97% | 39120 | 64 | 1 |
| OTU vs after mumu cleaning algorithm | 39120 | 57 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 45 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 41116 | 100 | 1 |
| OTU after vsearch reclustering at 97% | 41116 | 44 | 1 |
| OTU vs after mumu cleaning algorithm | 41116 | 43 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 32 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 19713 | 48 | 1 |
| OTU after vsearch reclustering at 97% | 19713 | 35 | 1 |
| OTU vs after mumu cleaning algorithm | 19713 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 30 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 47020 | 51 | 1 |
| OTU after vsearch reclustering at 97% | 47020 | 32 | 1 |
| OTU vs after mumu cleaning algorithm | 47020 | 30 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 26 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 42868 | 90 | 1 |
| OTU after vsearch reclustering at 97% | 42868 | 41 | 1 |
| OTU vs after mumu cleaning algorithm | 42868 | 38 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 31 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 36247 | 141 | 1 |
| OTU after vsearch reclustering at 97% | 36247 | 56 | 1 |
| OTU vs after mumu cleaning algorithm | 36247 | 51 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 41 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 49022 | 59 | 1 |
| OTU after vsearch reclustering at 97% | 49022 | 39 | 1 |
| OTU vs after mumu cleaning algorithm | 49022 | 36 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 42715 | 72 | 1 |
| OTU after vsearch reclustering at 97% | 42715 | 39 | 1 |
| OTU vs after mumu cleaning algorithm | 42715 | 35 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 30 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26291 | 48 | 1 |
| OTU after vsearch reclustering at 97% | 26291 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 26291 | 35 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 30 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 37604 | 69 | 1 |
| OTU after vsearch reclustering at 97% | 37604 | 39 | 1 |
| OTU vs after mumu cleaning algorithm | 37604 | 36 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 28 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 40928 | 106 | 1 |
| OTU after vsearch reclustering at 97% | 40928 | 63 | 1 |
| OTU vs after mumu cleaning algorithm | 40928 | 54 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 43 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 33952 | 51 | 1 |
| OTU after vsearch reclustering at 97% | 33952 | 35 | 1 |
| OTU vs after mumu cleaning algorithm | 33952 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 27 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 52285 | 62 | 1 |
| OTU after vsearch reclustering at 97% | 52285 | 27 | 1 |
| OTU vs after mumu cleaning algorithm | 52285 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 20 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 60215 | 64 | 1 |
| OTU after vsearch reclustering at 97% | 60215 | 32 | 1 |
| OTU vs after mumu cleaning algorithm | 60215 | 30 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 22 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 40260 | 81 | 1 |
| OTU after vsearch reclustering at 97% | 40260 | 54 | 1 |
| OTU vs after mumu cleaning algorithm | 40260 | 49 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 38 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 40299 | 55 | 1 |
| OTU after vsearch reclustering at 97% | 40299 | 37 | 1 |
| OTU vs after mumu cleaning algorithm | 40299 | 34 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 28 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 43012 | 77 | 1 |
| OTU after vsearch reclustering at 97% | 43012 | 47 | 1 |
| OTU vs after mumu cleaning algorithm | 43012 | 42 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 35 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 43587 | 38 | 1 |
| OTU after vsearch reclustering at 97% | 43587 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 43587 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 24 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 54450 | 19 | 1 |
| OTU after vsearch reclustering at 97% | 54450 | 14 | 1 |
| OTU vs after mumu cleaning algorithm | 54450 | 14 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 10 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 41464 | 53 | 1 |
| OTU after vsearch reclustering at 97% | 41464 | 39 | 1 |
| OTU vs after mumu cleaning algorithm | 41464 | 36 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 30 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 47495 | 45 | 1 |
| OTU after vsearch reclustering at 97% | 47495 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 47495 | 36 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 29 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 36764 | 13 | 1 |
| OTU after vsearch reclustering at 97% | 36764 | 11 | 1 |
| OTU vs after mumu cleaning algorithm | 36764 | 10 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 9 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 46627 | 55 | 1 |
| OTU after vsearch reclustering at 97% | 46627 | 35 | 1 |
| OTU vs after mumu cleaning algorithm | 46627 | 30 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26610 | 35 | 1 |
| OTU after vsearch reclustering at 97% | 26610 | 27 | 1 |
| OTU vs after mumu cleaning algorithm | 26610 | 25 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 19 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 42219 | 47 | 1 |
| OTU after vsearch reclustering at 97% | 42219 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 42219 | 29 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 20 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34581 | 57 | 1 |
| OTU after vsearch reclustering at 97% | 34581 | 33 | 1 |
| OTU vs after mumu cleaning algorithm | 34581 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 38263 | 43 | 1 |
| OTU after vsearch reclustering at 97% | 38263 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 38263 | 24 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 44632 | 45 | 1 |
| OTU after vsearch reclustering at 97% | 44632 | 32 | 1 |
| OTU vs after mumu cleaning algorithm | 44632 | 26 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 20 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34490 | 49 | 1 |
| OTU after vsearch reclustering at 97% | 34490 | 33 | 1 |
| OTU vs after mumu cleaning algorithm | 34490 | 30 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 26 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 38048 | 37 | 1 |
| OTU after vsearch reclustering at 97% | 38048 | 31 | 1 |
| OTU vs after mumu cleaning algorithm | 38048 | 31 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 26 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 45761 | 49 | 1 |
| OTU after vsearch reclustering at 97% | 45761 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 45761 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 18 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 46226 | 37 | 1 |
| OTU after vsearch reclustering at 97% | 46226 | 28 | 1 |
| OTU vs after mumu cleaning algorithm | 46226 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 43568 | 49 | 1 |
| OTU after vsearch reclustering at 97% | 43568 | 31 | 1 |
| OTU vs after mumu cleaning algorithm | 43568 | 22 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 20 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 38147 | 57 | 1 |
| OTU after vsearch reclustering at 97% | 38147 | 32 | 1 |
| OTU vs after mumu cleaning algorithm | 38147 | 24 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 37757 | 44 | 1 |
| OTU after vsearch reclustering at 97% | 37757 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 37757 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 32931 | 40 | 1 |
| OTU after vsearch reclustering at 97% | 32931 | 26 | 1 |
| OTU vs after mumu cleaning algorithm | 32931 | 22 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 32145 | 57 | 1 |
| OTU after vsearch reclustering at 97% | 32145 | 31 | 1 |
| OTU vs after mumu cleaning algorithm | 32145 | 24 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 22 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 44371 | 75 | 1 |
| OTU after vsearch reclustering at 97% | 44371 | 43 | 1 |
| OTU vs after mumu cleaning algorithm | 44371 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 22 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 50607 | 114 | 1 |
| OTU after vsearch reclustering at 97% | 50607 | 55 | 1 |
| OTU vs after mumu cleaning algorithm | 50607 | 48 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 42 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26575 | 46 | 1 |
| OTU after vsearch reclustering at 97% | 26575 | 28 | 1 |
| OTU vs after mumu cleaning algorithm | 26575 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 31404 | 91 | 1 |
| OTU after vsearch reclustering at 97% | 31404 | 43 | 1 |
| OTU vs after mumu cleaning algorithm | 31404 | 32 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 28 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 25805 | 49 | 1 |
| OTU after vsearch reclustering at 97% | 25805 | 37 | 1 |
| OTU vs after mumu cleaning algorithm | 25805 | 34 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 27 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 31504 | 40 | 1 |
| OTU after vsearch reclustering at 97% | 31504 | 29 | 1 |
| OTU vs after mumu cleaning algorithm | 31504 | 23 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 22 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 30917 | 66 | 1 |
| OTU after vsearch reclustering at 97% | 30917 | 37 | 1 |
| OTU vs after mumu cleaning algorithm | 30917 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 26 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 43064 | 54 | 1 |
| OTU after vsearch reclustering at 97% | 43064 | 33 | 1 |
| OTU vs after mumu cleaning algorithm | 43064 | 25 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 22 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34600 | 33 | 1 |
| OTU after vsearch reclustering at 97% | 34600 | 20 | 1 |
| OTU vs after mumu cleaning algorithm | 34600 | 15 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 13 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 43284 | 30 | 1 |
| OTU after vsearch reclustering at 97% | 43284 | 18 | 1 |
| OTU vs after mumu cleaning algorithm | 43284 | 16 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 12 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 37849 | 39 | 1 |
| OTU after vsearch reclustering at 97% | 37849 | 26 | 1 |
| OTU vs after mumu cleaning algorithm | 37849 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 17 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 37594 | 41 | 1 |
| OTU after vsearch reclustering at 97% | 37594 | 31 | 1 |
| OTU vs after mumu cleaning algorithm | 37594 | 22 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 47073 | 81 | 1 |
| OTU after vsearch reclustering at 97% | 47073 | 45 | 1 |
| OTU vs after mumu cleaning algorithm | 47073 | 43 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 35 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 32144 | 64 | 1 |
| OTU after vsearch reclustering at 97% | 32144 | 45 | 1 |
| OTU vs after mumu cleaning algorithm | 32144 | 38 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 35 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 36521 | 57 | 1 |
| OTU after vsearch reclustering at 97% | 36521 | 34 | 1 |
| OTU vs after mumu cleaning algorithm | 36521 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 39494 | 46 | 1 |
| OTU after vsearch reclustering at 97% | 39494 | 23 | 1 |
| OTU vs after mumu cleaning algorithm | 39494 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 14 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 41483 | 73 | 1 |
| OTU after vsearch reclustering at 97% | 41483 | 38 | 1 |
| OTU vs after mumu cleaning algorithm | 41483 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 28 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 45825 | 56 | 1 |
| OTU after vsearch reclustering at 97% | 45825 | 25 | 1 |
| OTU vs after mumu cleaning algorithm | 45825 | 21 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 18 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 30847 | 53 | 1 |
| OTU after vsearch reclustering at 97% | 30847 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 30847 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 24 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 38112 | 44 | 1 |
| OTU after vsearch reclustering at 97% | 38112 | 22 | 1 |
| OTU vs after mumu cleaning algorithm | 38112 | 17 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 15 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 35920 | 58 | 1 |
| OTU after vsearch reclustering at 97% | 35920 | 34 | 1 |
| OTU vs after mumu cleaning algorithm | 35920 | 25 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 20 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 16 | 2 | 1 |
| OTU after vsearch reclustering at 97% | 16 | 2 | 1 |
| OTU vs after mumu cleaning algorithm | 16 | 2 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 48901 | 78 | 1 |
| OTU after vsearch reclustering at 97% | 48901 | 40 | 1 |
| OTU vs after mumu cleaning algorithm | 48901 | 39 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 30151 | 57 | 1 |
| OTU after vsearch reclustering at 97% | 30151 | 38 | 1 |
| OTU vs after mumu cleaning algorithm | 30151 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 29 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 20514 | 51 | 1 |
| OTU after vsearch reclustering at 97% | 20514 | 27 | 1 |
| OTU vs after mumu cleaning algorithm | 20514 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 18 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 22220 | 38 | 1 |
| OTU after vsearch reclustering at 97% | 22220 | 28 | 1 |
| OTU vs after mumu cleaning algorithm | 22220 | 24 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34572 | 46 | 1 |
| OTU after vsearch reclustering at 97% | 34572 | 31 | 1 |
| OTU vs after mumu cleaning algorithm | 34572 | 24 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 20 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 24097 | 69 | 1 |
| OTU after vsearch reclustering at 97% | 24097 | 40 | 1 |
| OTU vs after mumu cleaning algorithm | 24097 | 32 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 27 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34532 | 55 | 1 |
| OTU after vsearch reclustering at 97% | 34532 | 34 | 1 |
| OTU vs after mumu cleaning algorithm | 34532 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 45735 | 82 | 1 |
| OTU after vsearch reclustering at 97% | 45735 | 47 | 1 |
| OTU vs after mumu cleaning algorithm | 45735 | 43 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 38 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 44652 | 70 | 1 |
| OTU after vsearch reclustering at 97% | 44652 | 39 | 1 |
| OTU vs after mumu cleaning algorithm | 44652 | 37 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 30 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 27522 | 84 | 1 |
| OTU after vsearch reclustering at 97% | 27522 | 75 | 1 |
| OTU vs after mumu cleaning algorithm | 27522 | 74 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 59 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 15209 | 86 | 1 |
| OTU after vsearch reclustering at 97% | 15209 | 68 | 1 |
| OTU vs after mumu cleaning algorithm | 15209 | 66 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 59 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34367 | 121 | 1 |
| OTU after vsearch reclustering at 97% | 34367 | 101 | 1 |
| OTU vs after mumu cleaning algorithm | 34367 | 97 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 77 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26010 | 129 | 1 |
| OTU after vsearch reclustering at 97% | 26010 | 116 | 1 |
| OTU vs after mumu cleaning algorithm | 26010 | 112 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 95 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 28215 | 234 | 1 |
| OTU after vsearch reclustering at 97% | 28215 | 219 | 1 |
| OTU vs after mumu cleaning algorithm | 28215 | 212 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 167 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 21612 | 143 | 1 |
| OTU after vsearch reclustering at 97% | 21612 | 126 | 1 |
| OTU vs after mumu cleaning algorithm | 21612 | 122 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 96 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 2654 | 62 | 1 |
| OTU after vsearch reclustering at 97% | 2654 | 62 | 1 |
| OTU vs after mumu cleaning algorithm | 2654 | 61 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 61 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 30110 | 208 | 1 |
| OTU after vsearch reclustering at 97% | 30110 | 186 | 1 |
| OTU vs after mumu cleaning algorithm | 30110 | 180 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 149 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 1706 | 69 | 1 |
| OTU after vsearch reclustering at 97% | 1706 | 69 | 1 |
| OTU vs after mumu cleaning algorithm | 1706 | 69 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 1289 | 31 | 1 |
| OTU after vsearch reclustering at 97% | 1289 | 31 | 1 |
| OTU vs after mumu cleaning algorithm | 1289 | 31 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 137 | 3 | 1 |
| OTU after vsearch reclustering at 97% | 137 | 3 | 1 |
| OTU vs after mumu cleaning algorithm | 137 | 3 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 10 | 1 | 1 |
| OTU after vsearch reclustering at 97% | 10 | 1 | 1 |
| OTU vs after mumu cleaning algorithm | 10 | 1 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 18171 | 140 | 1 |
| OTU after vsearch reclustering at 97% | 18171 | 128 | 1 |
| OTU vs after mumu cleaning algorithm | 18171 | 125 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 106 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 165 | 5 | 1 |
| OTU after vsearch reclustering at 97% | 165 | 5 | 1 |
| OTU vs after mumu cleaning algorithm | 165 | 5 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 5631 | 33 | 1 |
| OTU after vsearch reclustering at 97% | 5631 | 32 | 1 |
| OTU vs after mumu cleaning algorithm | 5631 | 32 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 32 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 4506 | 56 | 1 |
| OTU after vsearch reclustering at 97% | 4506 | 53 | 1 |
| OTU vs after mumu cleaning algorithm | 4506 | 52 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 50 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 5310 | 69 | 1 |
| OTU after vsearch reclustering at 97% | 5310 | 67 | 1 |
| OTU vs after mumu cleaning algorithm | 5310 | 67 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 64 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 4303 | 71 | 1 |
| OTU after vsearch reclustering at 97% | 4303 | 67 | 1 |
| OTU vs after mumu cleaning algorithm | 4303 | 67 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 67 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 11217 | 83 | 1 |
| OTU after vsearch reclustering at 97% | 11217 | 74 | 1 |
| OTU vs after mumu cleaning algorithm | 11217 | 73 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 65 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 27425 | 96 | 1 |
| OTU after vsearch reclustering at 97% | 27425 | 73 | 1 |
| OTU vs after mumu cleaning algorithm | 27425 | 71 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 58 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 879 | 13 | 1 |
| OTU after vsearch reclustering at 97% | 879 | 13 | 1 |
| OTU vs after mumu cleaning algorithm | 879 | 13 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 12587 | 79 | 1 |
| OTU after vsearch reclustering at 97% | 12587 | 72 | 1 |
| OTU vs after mumu cleaning algorithm | 12587 | 71 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 68 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 2360 | 41 | 1 |
| OTU after vsearch reclustering at 97% | 2360 | 41 | 1 |
| OTU vs after mumu cleaning algorithm | 2360 | 41 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 41 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 9558 | 92 | 1 |
| OTU after vsearch reclustering at 97% | 9558 | 90 | 1 |
| OTU vs after mumu cleaning algorithm | 9558 | 90 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 86 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 15373 | 130 | 1 |
| OTU after vsearch reclustering at 97% | 15373 | 118 | 1 |
| OTU vs after mumu cleaning algorithm | 15373 | 111 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 96 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 14987 | 135 | 1 |
| OTU after vsearch reclustering at 97% | 14987 | 131 | 1 |
| OTU vs after mumu cleaning algorithm | 14987 | 130 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 114 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 2563 | 47 | 1 |
| OTU after vsearch reclustering at 97% | 2563 | 47 | 1 |
| OTU vs after mumu cleaning algorithm | 2563 | 47 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 47 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 17690 | 161 | 1 |
| OTU after vsearch reclustering at 97% | 17690 | 150 | 1 |
| OTU vs after mumu cleaning algorithm | 17690 | 145 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 122 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 15226 | 122 | 1 |
| OTU after vsearch reclustering at 97% | 15226 | 119 | 1 |
| OTU vs after mumu cleaning algorithm | 15226 | 119 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 93 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 23986 | 115 | 1 |
| OTU after vsearch reclustering at 97% | 23986 | 104 | 1 |
| OTU vs after mumu cleaning algorithm | 23986 | 104 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 77 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 31340 | 286 | 1 |
| OTU after vsearch reclustering at 97% | 31340 | 265 | 1 |
| OTU vs after mumu cleaning algorithm | 31340 | 249 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 183 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 35527 | 8 | 1 |
| OTU after vsearch reclustering at 97% | 35527 | 7 | 1 |
| OTU vs after mumu cleaning algorithm | 35527 | 7 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 7 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 4650 | 5 | 1 |
| OTU after vsearch reclustering at 97% | 4650 | 4 | 1 |
| OTU vs after mumu cleaning algorithm | 4650 | 4 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 4 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 7256 | 21 | 1 |
| OTU after vsearch reclustering at 97% | 7256 | 18 | 1 |
| OTU vs after mumu cleaning algorithm | 7256 | 17 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 17 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 12411 | 38 | 1 |
| OTU after vsearch reclustering at 97% | 12411 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 12411 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 33 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 45849 | 25 | 1 |
| OTU after vsearch reclustering at 97% | 45849 | 21 | 1 |
| OTU vs after mumu cleaning algorithm | 45849 | 21 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 19 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 18577 | 75 | 1 |
| OTU after vsearch reclustering at 97% | 18577 | 63 | 1 |
| OTU vs after mumu cleaning algorithm | 18577 | 62 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 57 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 50601 | 62 | 1 |
| OTU after vsearch reclustering at 97% | 50601 | 35 | 1 |
| OTU vs after mumu cleaning algorithm | 50601 | 34 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 33 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 21202 | 83 | 1 |
| OTU after vsearch reclustering at 97% | 21202 | 61 | 1 |
| OTU vs after mumu cleaning algorithm | 21202 | 59 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 49 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 28703 | 130 | 1 |
| OTU after vsearch reclustering at 97% | 28703 | 106 | 1 |
| OTU vs after mumu cleaning algorithm | 28703 | 102 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 78 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 45701 | 40 | 1 |
| OTU after vsearch reclustering at 97% | 45701 | 23 | 1 |
| OTU vs after mumu cleaning algorithm | 45701 | 23 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 18799 | 156 | 1 |
| OTU after vsearch reclustering at 97% | 18799 | 144 | 1 |
| OTU vs after mumu cleaning algorithm | 18799 | 138 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 119 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 46508 | 32 | 1 |
| OTU after vsearch reclustering at 97% | 46508 | 24 | 1 |
| OTU vs after mumu cleaning algorithm | 46508 | 24 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 24 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26840 | 105 | 1 |
| OTU after vsearch reclustering at 97% | 26840 | 87 | 1 |
| OTU vs after mumu cleaning algorithm | 26840 | 85 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 78 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 52509 | 76 | 1 |
| OTU after vsearch reclustering at 97% | 52509 | 46 | 1 |
| OTU vs after mumu cleaning algorithm | 52509 | 40 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 35 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 53973 | 41 | 1 |
| OTU after vsearch reclustering at 97% | 53973 | 22 | 1 |
| OTU vs after mumu cleaning algorithm | 53973 | 21 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 16 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 35329 | 109 | 1 |
| OTU after vsearch reclustering at 97% | 35329 | 75 | 1 |
| OTU vs after mumu cleaning algorithm | 35329 | 74 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 61 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 50123 | 58 | 1 |
| OTU after vsearch reclustering at 97% | 50123 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 50123 | 29 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 27 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 9702 | 49 | 1 |
| OTU after vsearch reclustering at 97% | 9702 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 9702 | 36 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 32 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 44351 | 27 | 1 |
| OTU after vsearch reclustering at 97% | 44351 | 19 | 1 |
| OTU vs after mumu cleaning algorithm | 44351 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 17 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 11615 | 69 | 1 |
| OTU after vsearch reclustering at 97% | 11615 | 60 | 1 |
| OTU vs after mumu cleaning algorithm | 11615 | 60 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 54 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 39360 | 51 | 1 |
| OTU after vsearch reclustering at 97% | 39360 | 34 | 1 |
| OTU vs after mumu cleaning algorithm | 39360 | 34 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 34 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 14507 | 90 | 1 |
| OTU after vsearch reclustering at 97% | 14507 | 67 | 1 |
| OTU vs after mumu cleaning algorithm | 14507 | 65 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 55 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 41614 | 15 | 1 |
| OTU after vsearch reclustering at 97% | 41614 | 12 | 1 |
| OTU vs after mumu cleaning algorithm | 41614 | 11 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 11 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 23645 | 99 | 1 |
| OTU after vsearch reclustering at 97% | 23645 | 77 | 1 |
| OTU vs after mumu cleaning algorithm | 23645 | 77 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 61 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 47118 | 36 | 1 |
| OTU after vsearch reclustering at 97% | 47118 | 22 | 1 |
| OTU vs after mumu cleaning algorithm | 47118 | 22 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 20 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 20148 | 106 | 1 |
| OTU after vsearch reclustering at 97% | 20148 | 87 | 1 |
| OTU vs after mumu cleaning algorithm | 20148 | 87 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 73 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 54013 | 41 | 1 |
| OTU after vsearch reclustering at 97% | 54013 | 16 | 1 |
| OTU vs after mumu cleaning algorithm | 54013 | 16 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 16 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 17549 | 88 | 1 |
| OTU after vsearch reclustering at 97% | 17549 | 74 | 1 |
| OTU vs after mumu cleaning algorithm | 17549 | 72 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 60 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 47396 | 38 | 1 |
| OTU after vsearch reclustering at 97% | 47396 | 19 | 1 |
| OTU vs after mumu cleaning algorithm | 47396 | 18 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 18 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 21898 | 78 | 1 |
| OTU after vsearch reclustering at 97% | 21898 | 61 | 1 |
| OTU vs after mumu cleaning algorithm | 21898 | 61 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 55 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 51837 | 56 | 1 |
| OTU after vsearch reclustering at 97% | 51837 | 31 | 1 |
| OTU vs after mumu cleaning algorithm | 51837 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 28 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 19564 | 96 | 1 |
| OTU after vsearch reclustering at 97% | 19564 | 80 | 1 |
| OTU vs after mumu cleaning algorithm | 19564 | 77 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 66 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 25132 | 109 | 1 |
| OTU after vsearch reclustering at 97% | 25132 | 96 | 1 |
| OTU vs after mumu cleaning algorithm | 25132 | 95 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 80 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 49191 | 47 | 1 |
| OTU after vsearch reclustering at 97% | 49191 | 29 | 1 |
| OTU vs after mumu cleaning algorithm | 49191 | 26 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 24 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 24688 | 125 | 1 |
| OTU after vsearch reclustering at 97% | 24688 | 111 | 1 |
| OTU vs after mumu cleaning algorithm | 24688 | 106 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 90 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 52076 | 46 | 1 |
| OTU after vsearch reclustering at 97% | 52076 | 27 | 1 |
| OTU vs after mumu cleaning algorithm | 52076 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 23204 | 127 | 1 |
| OTU after vsearch reclustering at 97% | 23204 | 101 | 1 |
| OTU vs after mumu cleaning algorithm | 23204 | 95 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 80 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 43867 | 73 | 1 |
| OTU after vsearch reclustering at 97% | 43867 | 49 | 1 |
| OTU vs after mumu cleaning algorithm | 43867 | 48 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 41 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 50221 | 26 | 1 |
| OTU after vsearch reclustering at 97% | 50221 | 20 | 1 |
| OTU vs after mumu cleaning algorithm | 50221 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 18 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 31028 | 128 | 1 |
| OTU after vsearch reclustering at 97% | 31028 | 93 | 1 |
| OTU vs after mumu cleaning algorithm | 31028 | 91 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 66 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 114408 | 506 | 1 |
| OTU after vsearch reclustering at 97% | 114408 | 404 | 1 |
| OTU vs after mumu cleaning algorithm | 114408 | 387 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 217 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 108979 | 83 | 1 |
| OTU after vsearch reclustering at 97% | 108979 | 28 | 1 |
| OTU vs after mumu cleaning algorithm | 108979 | 23 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 20 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 95492 | 244 | 1 |
| OTU after vsearch reclustering at 97% | 95492 | 171 | 1 |
| OTU vs after mumu cleaning algorithm | 95492 | 169 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 95 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 77081 | 327 | 1 |
| OTU after vsearch reclustering at 97% | 77081 | 251 | 1 |
| OTU vs after mumu cleaning algorithm | 77081 | 242 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 143 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 70234 | 229 | 1 |
| OTU after vsearch reclustering at 97% | 70234 | 191 | 1 |
| OTU vs after mumu cleaning algorithm | 70234 | 188 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 124 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 111908 | 408 | 1 |
| OTU after vsearch reclustering at 97% | 111908 | 321 | 1 |
| OTU vs after mumu cleaning algorithm | 111908 | 310 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 164 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 85318 | 252 | 1 |
| OTU after vsearch reclustering at 97% | 85318 | 183 | 1 |
| OTU vs after mumu cleaning algorithm | 85318 | 177 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 159 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 100521 | 483 | 1 |
| OTU after vsearch reclustering at 97% | 100521 | 412 | 1 |
| OTU vs after mumu cleaning algorithm | 100521 | 389 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 203 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 67643 | 428 | 1 |
| OTU after vsearch reclustering at 97% | 67643 | 370 | 1 |
| OTU vs after mumu cleaning algorithm | 67643 | 356 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 216 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 68570 | 422 | 1 |
| OTU after vsearch reclustering at 97% | 68570 | 361 | 1 |
| OTU vs after mumu cleaning algorithm | 68570 | 342 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 209 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 89230 | 375 | 1 |
| OTU after vsearch reclustering at 97% | 89230 | 290 | 1 |
| OTU vs after mumu cleaning algorithm | 89230 | 269 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 156 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 104412 | 254 | 1 |
| OTU after vsearch reclustering at 97% | 104412 | 179 | 1 |
| OTU vs after mumu cleaning algorithm | 104412 | 177 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 148 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 72829 | 437 | 1 |
| OTU after vsearch reclustering at 97% | 72829 | 380 | 1 |
| OTU vs after mumu cleaning algorithm | 72829 | 357 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 213 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 78311 | 361 | 1 |
| OTU after vsearch reclustering at 97% | 78311 | 314 | 1 |
| OTU vs after mumu cleaning algorithm | 78311 | 302 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 189 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 58171 | 273 | 1 |
| OTU after vsearch reclustering at 97% | 58171 | 235 | 1 |
| OTU vs after mumu cleaning algorithm | 58171 | 228 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 178 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 65804 | 289 | 1 |
| OTU after vsearch reclustering at 97% | 65804 | 228 | 1 |
| OTU vs after mumu cleaning algorithm | 65804 | 224 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 156 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 101861 | 318 | 1 |
| OTU after vsearch reclustering at 97% | 101861 | 246 | 1 |
| OTU vs after mumu cleaning algorithm | 101861 | 236 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 144 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 113682 | 419 | 1 |
| OTU after vsearch reclustering at 97% | 113682 | 378 | 1 |
| OTU vs after mumu cleaning algorithm | 113682 | 358 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 174 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 74180 | 160 | 1 |
| OTU after vsearch reclustering at 97% | 74180 | 129 | 1 |
| OTU vs after mumu cleaning algorithm | 74180 | 124 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 119 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 46508 | 36 | 1 |
| OTU after vsearch reclustering at 97% | 46508 | 22 | 1 |
| OTU vs after mumu cleaning algorithm | 46508 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 16 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 61154 | 95 | 1 |
| OTU after vsearch reclustering at 97% | 61154 | 57 | 1 |
| OTU vs after mumu cleaning algorithm | 61154 | 52 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 49 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 95979 | 451 | 1 |
| OTU after vsearch reclustering at 97% | 95979 | 377 | 1 |
| OTU vs after mumu cleaning algorithm | 95979 | 359 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 276 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 135539 | 313 | 1 |
| OTU after vsearch reclustering at 97% | 135539 | 285 | 1 |
| OTU vs after mumu cleaning algorithm | 135539 | 265 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 132 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 100007 | 479 | 1 |
| OTU after vsearch reclustering at 97% | 100007 | 414 | 1 |
| OTU vs after mumu cleaning algorithm | 100007 | 397 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 205 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 83355 | 274 | 1 |
| OTU after vsearch reclustering at 97% | 83355 | 191 | 1 |
| OTU vs after mumu cleaning algorithm | 83355 | 183 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 156 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 60422 | 323 | 1 |
| OTU after vsearch reclustering at 97% | 60422 | 284 | 1 |
| OTU vs after mumu cleaning algorithm | 60422 | 267 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 185 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 65476 | 350 | 1 |
| OTU after vsearch reclustering at 97% | 65476 | 312 | 1 |
| OTU vs after mumu cleaning algorithm | 65476 | 297 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 213 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 41460 | 37 | 1 |
| OTU after vsearch reclustering at 97% | 41460 | 26 | 1 |
| OTU vs after mumu cleaning algorithm | 41460 | 26 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 26 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 15023 | 74 | 1 |
| OTU after vsearch reclustering at 97% | 15023 | 62 | 1 |
| OTU vs after mumu cleaning algorithm | 15023 | 60 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 55 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 46031 | 44 | 1 |
| OTU after vsearch reclustering at 97% | 46031 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 46031 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 11896 | 41 | 1 |
| OTU after vsearch reclustering at 97% | 11896 | 28 | 1 |
| OTU vs after mumu cleaning algorithm | 11896 | 26 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 24 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 32984 | 62 | 1 |
| OTU after vsearch reclustering at 97% | 32984 | 38 | 1 |
| OTU vs after mumu cleaning algorithm | 32984 | 35 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 31 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 14288 | 67 | 1 |
| OTU after vsearch reclustering at 97% | 14288 | 44 | 1 |
| OTU vs after mumu cleaning algorithm | 14288 | 43 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 40 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 56729 | 32 | 1 |
| OTU after vsearch reclustering at 97% | 56729 | 22 | 1 |
| OTU vs after mumu cleaning algorithm | 56729 | 22 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 16293 | 58 | 1 |
| OTU after vsearch reclustering at 97% | 16293 | 39 | 1 |
| OTU vs after mumu cleaning algorithm | 16293 | 39 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 31 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 55279 | 60 | 1 |
| OTU after vsearch reclustering at 97% | 55279 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 55279 | 35 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 34 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 22683 | 83 | 1 |
| OTU after vsearch reclustering at 97% | 22683 | 65 | 1 |
| OTU vs after mumu cleaning algorithm | 22683 | 65 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 49 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 23988 | 75 | 1 |
| OTU after vsearch reclustering at 97% | 23988 | 60 | 1 |
| OTU vs after mumu cleaning algorithm | 23988 | 53 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 38 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 42957 | 73 | 1 |
| OTU after vsearch reclustering at 97% | 42957 | 49 | 1 |
| OTU vs after mumu cleaning algorithm | 42957 | 46 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 40 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 27619 | 67 | 1 |
| OTU after vsearch reclustering at 97% | 27619 | 49 | 1 |
| OTU vs after mumu cleaning algorithm | 27619 | 46 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 41 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 43754 | 67 | 1 |
| OTU after vsearch reclustering at 97% | 43754 | 34 | 1 |
| OTU vs after mumu cleaning algorithm | 43754 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 29 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 18817 | 83 | 1 |
| OTU after vsearch reclustering at 97% | 18817 | 67 | 1 |
| OTU vs after mumu cleaning algorithm | 18817 | 66 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 56 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 24707 | 131 | 1 |
| OTU after vsearch reclustering at 97% | 24707 | 111 | 1 |
| OTU vs after mumu cleaning algorithm | 24707 | 106 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 95 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 57703 | 41 | 1 |
| OTU after vsearch reclustering at 97% | 57703 | 24 | 1 |
| OTU vs after mumu cleaning algorithm | 57703 | 22 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 19 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 49527 | 57 | 1 |
| OTU after vsearch reclustering at 97% | 49527 | 33 | 1 |
| OTU vs after mumu cleaning algorithm | 49527 | 31 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 28 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 32563 | 110 | 1 |
| OTU after vsearch reclustering at 97% | 32563 | 77 | 1 |
| OTU vs after mumu cleaning algorithm | 32563 | 74 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 50 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 48395 | 51 | 1 |
| OTU after vsearch reclustering at 97% | 48395 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 48395 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 26 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 44030 | 55 | 1 |
| OTU after vsearch reclustering at 97% | 44030 | 41 | 1 |
| OTU vs after mumu cleaning algorithm | 44030 | 39 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 39 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 35291 | 134 | 1 |
| OTU after vsearch reclustering at 97% | 35291 | 92 | 1 |
| OTU vs after mumu cleaning algorithm | 35291 | 87 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 64 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 53352 | 59 | 1 |
| OTU after vsearch reclustering at 97% | 53352 | 35 | 1 |
| OTU vs after mumu cleaning algorithm | 53352 | 32 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 27 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 9036 | 35 | 1 |
| OTU after vsearch reclustering at 97% | 9036 | 28 | 1 |
| OTU vs after mumu cleaning algorithm | 9036 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 27 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 46764 | 56 | 1 |
| OTU after vsearch reclustering at 97% | 46764 | 29 | 1 |
| OTU vs after mumu cleaning algorithm | 46764 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 9834 | 72 | 1 |
| OTU after vsearch reclustering at 97% | 9834 | 61 | 1 |
| OTU vs after mumu cleaning algorithm | 9834 | 58 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 52 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 52197 | 73 | 1 |
| OTU after vsearch reclustering at 97% | 52197 | 37 | 1 |
| OTU vs after mumu cleaning algorithm | 52197 | 34 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 31 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 14600 | 66 | 1 |
| OTU after vsearch reclustering at 97% | 14600 | 56 | 1 |
| OTU vs after mumu cleaning algorithm | 14600 | 56 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 48 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 39259 | 35 | 1 |
| OTU after vsearch reclustering at 97% | 39259 | 27 | 1 |
| OTU vs after mumu cleaning algorithm | 39259 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 19234 | 91 | 1 |
| OTU after vsearch reclustering at 97% | 19234 | 74 | 1 |
| OTU vs after mumu cleaning algorithm | 19234 | 70 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 55 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 49636 | 38 | 1 |
| OTU after vsearch reclustering at 97% | 49636 | 23 | 1 |
| OTU vs after mumu cleaning algorithm | 49636 | 22 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 24948 | 117 | 1 |
| OTU after vsearch reclustering at 97% | 24948 | 93 | 1 |
| OTU vs after mumu cleaning algorithm | 24948 | 90 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 80 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 56903 | 70 | 1 |
| OTU after vsearch reclustering at 97% | 56903 | 28 | 1 |
| OTU vs after mumu cleaning algorithm | 56903 | 26 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 22848 | 52 | 1 |
| OTU after vsearch reclustering at 97% | 22848 | 44 | 1 |
| OTU vs after mumu cleaning algorithm | 22848 | 43 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 33 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 22571 | 140 | 1 |
| OTU after vsearch reclustering at 97% | 22571 | 110 | 1 |
| OTU vs after mumu cleaning algorithm | 22571 | 109 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 90 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 7144 | 119 | 1 |
| OTU after vsearch reclustering at 97% | 7144 | 117 | 1 |
| OTU vs after mumu cleaning algorithm | 7144 | 113 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 107 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 2407 | 65 | 1 |
| OTU after vsearch reclustering at 97% | 2407 | 65 | 1 |
| OTU vs after mumu cleaning algorithm | 2407 | 65 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 65 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 32327 | 213 | 1 |
| OTU after vsearch reclustering at 97% | 32327 | 186 | 1 |
| OTU vs after mumu cleaning algorithm | 32327 | 182 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 124 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 22968 | 89 | 1 |
| OTU after vsearch reclustering at 97% | 22968 | 66 | 1 |
| OTU vs after mumu cleaning algorithm | 22968 | 66 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 58 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 7161 | 148 | 1 |
| OTU after vsearch reclustering at 97% | 7161 | 143 | 1 |
| OTU vs after mumu cleaning algorithm | 7161 | 139 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 132 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 6208 | 26 | 1 |
| OTU after vsearch reclustering at 97% | 6208 | 23 | 1 |
| OTU vs after mumu cleaning algorithm | 6208 | 23 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 12314 | 102 | 1 |
| OTU after vsearch reclustering at 97% | 12314 | 94 | 1 |
| OTU vs after mumu cleaning algorithm | 12314 | 92 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 75 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 33750 | 220 | 1 |
| OTU after vsearch reclustering at 97% | 33750 | 178 | 1 |
| OTU vs after mumu cleaning algorithm | 33750 | 171 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 115 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26302 | 184 | 1 |
| OTU after vsearch reclustering at 97% | 26302 | 154 | 1 |
| OTU vs after mumu cleaning algorithm | 26302 | 153 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 118 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 21363 | 232 | 1 |
| OTU after vsearch reclustering at 97% | 21363 | 220 | 1 |
| OTU vs after mumu cleaning algorithm | 21363 | 214 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 172 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 25560 | 226 | 1 |
| OTU after vsearch reclustering at 97% | 25560 | 208 | 1 |
| OTU vs after mumu cleaning algorithm | 25560 | 207 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 163 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 33146 | 319 | 1 |
| OTU after vsearch reclustering at 97% | 33146 | 285 | 1 |
| OTU vs after mumu cleaning algorithm | 33146 | 279 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 215 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 8285 | 159 | 1 |
| OTU after vsearch reclustering at 97% | 8285 | 150 | 1 |
| OTU vs after mumu cleaning algorithm | 8285 | 146 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 145 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 2273 | 22 | 1 |
| OTU after vsearch reclustering at 97% | 2273 | 22 | 1 |
| OTU vs after mumu cleaning algorithm | 2273 | 22 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 185 | 8 | 1 |
| OTU after vsearch reclustering at 97% | 185 | 8 | 1 |
| OTU vs after mumu cleaning algorithm | 185 | 8 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 13488 | 59 | 1 |
| OTU after vsearch reclustering at 97% | 13488 | 56 | 1 |
| OTU vs after mumu cleaning algorithm | 13488 | 56 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 49 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 508 | 6 | 1 |
| OTU after vsearch reclustering at 97% | 508 | 6 | 1 |
| OTU vs after mumu cleaning algorithm | 508 | 6 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 9993 | 139 | 1 |
| OTU after vsearch reclustering at 97% | 9993 | 134 | 1 |
| OTU vs after mumu cleaning algorithm | 9993 | 132 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 116 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 211 | 9 | 1 |
| OTU after vsearch reclustering at 97% | 211 | 9 | 1 |
| OTU vs after mumu cleaning algorithm | 211 | 9 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 1370 | 52 | 1 |
| OTU after vsearch reclustering at 97% | 1370 | 52 | 1 |
| OTU vs after mumu cleaning algorithm | 1370 | 52 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 4383 | 82 | 1 |
| OTU after vsearch reclustering at 97% | 4383 | 81 | 1 |
| OTU vs after mumu cleaning algorithm | 4383 | 78 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 78 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 39769 | 88 | 1 |
| OTU after vsearch reclustering at 97% | 39769 | 60 | 1 |
| OTU vs after mumu cleaning algorithm | 39769 | 59 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 42 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 0 | 15832 | 1 |
| OTU after vsearch reclustering at 97% | 0 | 6679 | 1 |
| OTU vs after mumu cleaning algorithm | 0 | 0 | 0 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 4043 | 84 | 1 |
| OTU after vsearch reclustering at 97% | 4043 | 81 | 1 |
| OTU vs after mumu cleaning algorithm | 4043 | 81 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 81 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 1038 | 19 | 1 |
| OTU after vsearch reclustering at 97% | 1038 | 19 | 1 |
| OTU vs after mumu cleaning algorithm | 1038 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 25032 | 164 | 1 |
| OTU after vsearch reclustering at 97% | 25032 | 153 | 1 |
| OTU vs after mumu cleaning algorithm | 25032 | 153 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 127 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26341 | 144 | 1 |
| OTU after vsearch reclustering at 97% | 26341 | 127 | 1 |
| OTU vs after mumu cleaning algorithm | 26341 | 123 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 104 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 571 | 10 | 1 |
| OTU after vsearch reclustering at 97% | 571 | 9 | 1 |
| OTU vs after mumu cleaning algorithm | 571 | 9 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 771 | 20 | 1 |
| OTU after vsearch reclustering at 97% | 771 | 19 | 1 |
| OTU vs after mumu cleaning algorithm | 771 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34353 | 152 | 1 |
| OTU after vsearch reclustering at 97% | 34353 | 117 | 1 |
| OTU vs after mumu cleaning algorithm | 34353 | 111 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 89 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 31503 | 245 | 1 |
| OTU after vsearch reclustering at 97% | 31503 | 227 | 1 |
| OTU vs after mumu cleaning algorithm | 31503 | 214 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 167 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 29060 | 142 | 1 |
| OTU after vsearch reclustering at 97% | 29060 | 128 | 1 |
| OTU vs after mumu cleaning algorithm | 29060 | 120 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 95 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 2963 | 68 | 1 |
| OTU after vsearch reclustering at 97% | 2963 | 66 | 1 |
| OTU vs after mumu cleaning algorithm | 2963 | 64 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 61 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26475 | 125 | 1 |
| OTU after vsearch reclustering at 97% | 26475 | 108 | 1 |
| OTU vs after mumu cleaning algorithm | 26475 | 107 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 79 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 7170 | 77 | 1 |
| OTU after vsearch reclustering at 97% | 7170 | 73 | 1 |
| OTU vs after mumu cleaning algorithm | 7170 | 72 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 67 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 21658 | 139 | 1 |
| OTU after vsearch reclustering at 97% | 21658 | 124 | 1 |
| OTU vs after mumu cleaning algorithm | 21658 | 123 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 91 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 12383 | 183 | 1 |
| OTU after vsearch reclustering at 97% | 12383 | 172 | 1 |
| OTU vs after mumu cleaning algorithm | 12383 | 170 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 143 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 14590 | 105 | 1 |
| OTU after vsearch reclustering at 97% | 14590 | 102 | 1 |
| OTU vs after mumu cleaning algorithm | 14590 | 101 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 76 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 29375 | 240 | 1 |
| OTU after vsearch reclustering at 97% | 29375 | 209 | 1 |
| OTU vs after mumu cleaning algorithm | 29375 | 207 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 159 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 39476 | 249 | 1 |
| OTU after vsearch reclustering at 97% | 39476 | 215 | 1 |
| OTU vs after mumu cleaning algorithm | 39476 | 207 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 145 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 48251 | 196 | 1 |
| OTU after vsearch reclustering at 97% | 48251 | 155 | 1 |
| OTU vs after mumu cleaning algorithm | 48251 | 152 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 110 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 65841 | 207 | 1 |
| OTU after vsearch reclustering at 97% | 65841 | 163 | 1 |
| OTU vs after mumu cleaning algorithm | 65841 | 155 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 96 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 56755 | 176 | 1 |
| OTU after vsearch reclustering at 97% | 56755 | 140 | 1 |
| OTU vs after mumu cleaning algorithm | 56755 | 134 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 89 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 63892 | 265 | 1 |
| OTU after vsearch reclustering at 97% | 63892 | 220 | 1 |
| OTU vs after mumu cleaning algorithm | 63892 | 211 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 130 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26416 | 295 | 1 |
| OTU after vsearch reclustering at 97% | 26416 | 282 | 1 |
| OTU vs after mumu cleaning algorithm | 26416 | 274 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 206 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 32097 | 235 | 1 |
| OTU after vsearch reclustering at 97% | 32097 | 225 | 1 |
| OTU vs after mumu cleaning algorithm | 32097 | 219 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 158 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 56835 | 180 | 1 |
| OTU after vsearch reclustering at 97% | 56835 | 131 | 1 |
| OTU vs after mumu cleaning algorithm | 56835 | 130 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 87 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 49250 | 257 | 1 |
| OTU after vsearch reclustering at 97% | 49250 | 209 | 1 |
| OTU vs after mumu cleaning algorithm | 49250 | 206 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 144 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 29265 | 231 | 1 |
| OTU after vsearch reclustering at 97% | 29265 | 214 | 1 |
| OTU vs after mumu cleaning algorithm | 29265 | 213 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 156 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 56552 | 294 | 1 |
| OTU after vsearch reclustering at 97% | 56552 | 247 | 1 |
| OTU vs after mumu cleaning algorithm | 56552 | 240 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 156 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 120864 | 137 | 1 |
| OTU after vsearch reclustering at 97% | 120864 | 85 | 1 |
| OTU vs after mumu cleaning algorithm | 120864 | 79 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 71 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 156033 | 128 | 1 |
| OTU after vsearch reclustering at 97% | 156033 | 29 | 1 |
| OTU vs after mumu cleaning algorithm | 156033 | 26 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 81013 | 85 | 1 |
| OTU after vsearch reclustering at 97% | 81013 | 51 | 1 |
| OTU vs after mumu cleaning algorithm | 81013 | 49 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 48 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 68263 | 197 | 1 |
| OTU after vsearch reclustering at 97% | 68263 | 143 | 1 |
| OTU vs after mumu cleaning algorithm | 68263 | 133 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 115 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 66093 | 419 | 1 |
| OTU after vsearch reclustering at 97% | 66093 | 376 | 1 |
| OTU vs after mumu cleaning algorithm | 66093 | 366 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 251 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 107836 | 435 | 1 |
| OTU after vsearch reclustering at 97% | 107836 | 357 | 1 |
| OTU vs after mumu cleaning algorithm | 107836 | 331 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 164 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 90244 | 320 | 1 |
| OTU after vsearch reclustering at 97% | 90244 | 222 | 1 |
| OTU vs after mumu cleaning algorithm | 90244 | 213 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 134 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 130809 | 515 | 1 |
| OTU after vsearch reclustering at 97% | 130809 | 443 | 1 |
| OTU vs after mumu cleaning algorithm | 130809 | 413 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 224 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 90110 | 526 | 1 |
| OTU after vsearch reclustering at 97% | 90110 | 441 | 1 |
| OTU vs after mumu cleaning algorithm | 90110 | 417 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 262 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 99141 | 319 | 1 |
| OTU after vsearch reclustering at 97% | 99141 | 245 | 1 |
| OTU vs after mumu cleaning algorithm | 99141 | 237 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 135 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 62575 | 263 | 1 |
| OTU after vsearch reclustering at 97% | 62575 | 201 | 1 |
| OTU vs after mumu cleaning algorithm | 62575 | 199 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 134 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 50583 | 80 | 1 |
| OTU after vsearch reclustering at 97% | 50583 | 17 | 1 |
| OTU vs after mumu cleaning algorithm | 50583 | 17 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 15 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 39213 | 148 | 1 |
| OTU after vsearch reclustering at 97% | 39213 | 105 | 1 |
| OTU vs after mumu cleaning algorithm | 39213 | 103 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 87 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 37200 | 97 | 1 |
| OTU after vsearch reclustering at 97% | 37200 | 67 | 1 |
| OTU vs after mumu cleaning algorithm | 37200 | 64 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 54 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 41451 | 27 | 1 |
| OTU after vsearch reclustering at 97% | 41451 | 21 | 1 |
| OTU vs after mumu cleaning algorithm | 41451 | 21 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 18 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 33334 | 208 | 1 |
| OTU after vsearch reclustering at 97% | 33334 | 170 | 1 |
| OTU vs after mumu cleaning algorithm | 33334 | 164 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 115 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 33197 | 116 | 1 |
| OTU after vsearch reclustering at 97% | 33197 | 91 | 1 |
| OTU vs after mumu cleaning algorithm | 33197 | 84 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 68 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 56532 | 73 | 1 |
| OTU after vsearch reclustering at 97% | 56532 | 38 | 1 |
| OTU vs after mumu cleaning algorithm | 56532 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 30 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 30498 | 135 | 1 |
| OTU after vsearch reclustering at 97% | 30498 | 125 | 1 |
| OTU vs after mumu cleaning algorithm | 30498 | 123 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 108 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 37295 | 151 | 1 |
| OTU after vsearch reclustering at 97% | 37295 | 126 | 1 |
| OTU vs after mumu cleaning algorithm | 37295 | 117 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 94 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 54042 | 34 | 1 |
| OTU after vsearch reclustering at 97% | 54042 | 19 | 1 |
| OTU vs after mumu cleaning algorithm | 54042 | 14 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 13 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 13889 | 83 | 1 |
| OTU after vsearch reclustering at 97% | 13889 | 79 | 1 |
| OTU vs after mumu cleaning algorithm | 13889 | 74 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 67 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 31231 | 107 | 1 |
| OTU after vsearch reclustering at 97% | 31231 | 94 | 1 |
| OTU vs after mumu cleaning algorithm | 31231 | 91 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 72 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 23281 | 29 | 1 |
| OTU after vsearch reclustering at 97% | 23281 | 17 | 1 |
| OTU vs after mumu cleaning algorithm | 23281 | 17 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 17 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 14591 | 62 | 1 |
| OTU after vsearch reclustering at 97% | 14591 | 55 | 1 |
| OTU vs after mumu cleaning algorithm | 14591 | 53 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 41 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 30748 | 109 | 1 |
| OTU after vsearch reclustering at 97% | 30748 | 82 | 1 |
| OTU vs after mumu cleaning algorithm | 30748 | 81 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 62 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 44997 | 33 | 1 |
| OTU after vsearch reclustering at 97% | 44997 | 19 | 1 |
| OTU vs after mumu cleaning algorithm | 44997 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 19 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 18651 | 105 | 1 |
| OTU after vsearch reclustering at 97% | 18651 | 96 | 1 |
| OTU vs after mumu cleaning algorithm | 18651 | 94 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 75 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 26947 | 78 | 1 |
| OTU after vsearch reclustering at 97% | 26947 | 61 | 1 |
| OTU vs after mumu cleaning algorithm | 26947 | 60 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 54 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 36843 | 27 | 1 |
| OTU after vsearch reclustering at 97% | 36843 | 23 | 1 |
| OTU vs after mumu cleaning algorithm | 36843 | 23 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 23 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 12759 | 70 | 1 |
| OTU after vsearch reclustering at 97% | 12759 | 64 | 1 |
| OTU vs after mumu cleaning algorithm | 12759 | 62 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 50 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 28982 | 92 | 1 |
| OTU after vsearch reclustering at 97% | 28982 | 65 | 1 |
| OTU vs after mumu cleaning algorithm | 28982 | 63 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 47 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 53722 | 63 | 1 |
| OTU after vsearch reclustering at 97% | 53722 | 32 | 1 |
| OTU vs after mumu cleaning algorithm | 53722 | 31 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 27 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 10564 | 39 | 1 |
| OTU after vsearch reclustering at 97% | 10564 | 28 | 1 |
| OTU vs after mumu cleaning algorithm | 10564 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 28 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 40396 | 86 | 1 |
| OTU after vsearch reclustering at 97% | 40396 | 53 | 1 |
| OTU vs after mumu cleaning algorithm | 40396 | 49 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 38 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 46803 | 53 | 1 |
| OTU after vsearch reclustering at 97% | 46803 | 26 | 1 |
| OTU vs after mumu cleaning algorithm | 46803 | 25 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 9679 | 43 | 1 |
| OTU after vsearch reclustering at 97% | 9679 | 40 | 1 |
| OTU vs after mumu cleaning algorithm | 9679 | 39 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 38 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 5903 | 38 | 1 |
| OTU after vsearch reclustering at 97% | 5903 | 34 | 1 |
| OTU vs after mumu cleaning algorithm | 5903 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 32 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 54738 | 48 | 1 |
| OTU after vsearch reclustering at 97% | 54738 | 27 | 1 |
| OTU vs after mumu cleaning algorithm | 54738 | 25 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 21 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 21071 | 68 | 1 |
| OTU after vsearch reclustering at 97% | 21071 | 56 | 1 |
| OTU vs after mumu cleaning algorithm | 21071 | 54 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 45 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 19991 | 51 | 1 |
| OTU after vsearch reclustering at 97% | 19991 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 19991 | 34 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 31 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 50305 | 34 | 1 |
| OTU after vsearch reclustering at 97% | 50305 | 19 | 1 |
| OTU vs after mumu cleaning algorithm | 50305 | 18 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 18 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 15894 | 66 | 1 |
| OTU after vsearch reclustering at 97% | 15894 | 55 | 1 |
| OTU vs after mumu cleaning algorithm | 15894 | 53 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 46 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 23843 | 110 | 1 |
| OTU after vsearch reclustering at 97% | 23843 | 97 | 1 |
| OTU vs after mumu cleaning algorithm | 23843 | 96 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 87 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 42198 | 58 | 1 |
| OTU after vsearch reclustering at 97% | 42198 | 38 | 1 |
| OTU vs after mumu cleaning algorithm | 42198 | 34 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 32 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 18677 | 72 | 1 |
| OTU after vsearch reclustering at 97% | 18677 | 61 | 1 |
| OTU vs after mumu cleaning algorithm | 18677 | 60 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 48 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 24643 | 118 | 1 |
| OTU after vsearch reclustering at 97% | 24643 | 98 | 1 |
| OTU vs after mumu cleaning algorithm | 24643 | 97 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 87 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 52579 | 56 | 1 |
| OTU after vsearch reclustering at 97% | 52579 | 37 | 1 |
| OTU vs after mumu cleaning algorithm | 52579 | 35 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 30 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 29735 | 92 | 1 |
| OTU after vsearch reclustering at 97% | 29735 | 67 | 1 |
| OTU vs after mumu cleaning algorithm | 29735 | 64 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 54 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 30257 | 60 | 1 |
| OTU after vsearch reclustering at 97% | 30257 | 46 | 1 |
| OTU vs after mumu cleaning algorithm | 30257 | 46 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 42 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 49966 | 47 | 1 |
| OTU after vsearch reclustering at 97% | 49966 | 35 | 1 |
| OTU vs after mumu cleaning algorithm | 49966 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 29 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 40636 | 86 | 1 |
| OTU after vsearch reclustering at 97% | 40636 | 76 | 1 |
| OTU vs after mumu cleaning algorithm | 40636 | 73 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 49 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34493 | 58 | 1 |
| OTU after vsearch reclustering at 97% | 34493 | 48 | 1 |
| OTU vs after mumu cleaning algorithm | 34493 | 47 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 36 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 52371 | 48 | 1 |
| OTU after vsearch reclustering at 97% | 52371 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 52371 | 36 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 35 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 40526 | 95 | 1 |
| OTU after vsearch reclustering at 97% | 40526 | 61 | 1 |
| OTU vs after mumu cleaning algorithm | 40526 | 60 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 52 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 31521 | 92 | 1 |
| OTU after vsearch reclustering at 97% | 31521 | 71 | 1 |
| OTU vs after mumu cleaning algorithm | 31521 | 67 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 58 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 45552 | 36 | 1 |
| OTU after vsearch reclustering at 97% | 45552 | 18 | 1 |
| OTU vs after mumu cleaning algorithm | 45552 | 18 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 17 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 28256 | 50 | 1 |
| OTU after vsearch reclustering at 97% | 28256 | 44 | 1 |
| OTU vs after mumu cleaning algorithm | 28256 | 43 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 39 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 32987 | 68 | 1 |
| OTU after vsearch reclustering at 97% | 32987 | 52 | 1 |
| OTU vs after mumu cleaning algorithm | 32987 | 48 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 42 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 39947 | 63 | 1 |
| OTU after vsearch reclustering at 97% | 39947 | 38 | 1 |
| OTU vs after mumu cleaning algorithm | 39947 | 35 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 34 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 33495 | 52 | 1 |
| OTU after vsearch reclustering at 97% | 33495 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 33495 | 36 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 34 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 34586 | 100 | 1 |
| OTU after vsearch reclustering at 97% | 34586 | 82 | 1 |
| OTU vs after mumu cleaning algorithm | 34586 | 75 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 68 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 57322 | 45 | 1 |
| OTU after vsearch reclustering at 97% | 57322 | 29 | 1 |
| OTU vs after mumu cleaning algorithm | 57322 | 28 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 26 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 36281 | 133 | 1 |
| OTU after vsearch reclustering at 97% | 36281 | 102 | 1 |
| OTU vs after mumu cleaning algorithm | 36281 | 97 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 89 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 29827 | 127 | 1 |
| OTU after vsearch reclustering at 97% | 29827 | 104 | 1 |
| OTU vs after mumu cleaning algorithm | 29827 | 103 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 93 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 47018 | 49 | 1 |
| OTU after vsearch reclustering at 97% | 47018 | 36 | 1 |
| OTU vs after mumu cleaning algorithm | 47018 | 34 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 31 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 2 | 1 | 1 |
| OTU after vsearch reclustering at 97% | 2 | 1 | 1 |
| OTU vs after mumu cleaning algorithm | 2 | 1 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 31672 | 186 | 1 |
| OTU after vsearch reclustering at 97% | 31672 | 164 | 1 |
| OTU vs after mumu cleaning algorithm | 31672 | 159 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 114 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 49324 | 32 | 1 |
| OTU after vsearch reclustering at 97% | 49324 | 19 | 1 |
| OTU vs after mumu cleaning algorithm | 49324 | 19 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 17 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 25083 | 96 | 1 |
| OTU after vsearch reclustering at 97% | 25083 | 85 | 1 |
| OTU vs after mumu cleaning algorithm | 25083 | 83 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 65 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 30839 | 139 | 1 |
| OTU after vsearch reclustering at 97% | 30839 | 127 | 1 |
| OTU vs after mumu cleaning algorithm | 30839 | 122 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 83 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 23423 | 51 | 1 |
| OTU after vsearch reclustering at 97% | 23423 | 25 | 1 |
| OTU vs after mumu cleaning algorithm | 23423 | 25 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 24 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 13 | 2 | 1 |
| OTU after vsearch reclustering at 97% | 13 | 2 | 1 |
| OTU vs after mumu cleaning algorithm | 13 | 2 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 54989 | 56 | 1 |
| OTU after vsearch reclustering at 97% | 54989 | 31 | 1 |
| OTU vs after mumu cleaning algorithm | 54989 | 30 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 30 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 240 | 18 | 1 |
| OTU after vsearch reclustering at 97% | 240 | 18 | 1 |
| OTU vs after mumu cleaning algorithm | 240 | 18 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 0 | 0 | 0 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 60325 | 54 | 1 |
| OTU after vsearch reclustering at 97% | 60325 | 30 | 1 |
| OTU vs after mumu cleaning algorithm | 60325 | 27 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 27 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 13869 | 88 | 1 |
| OTU after vsearch reclustering at 97% | 13869 | 80 | 1 |
| OTU vs after mumu cleaning algorithm | 13869 | 76 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 63 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 18751 | 117 | 1 |
| OTU after vsearch reclustering at 97% | 18751 | 105 | 1 |
| OTU vs after mumu cleaning algorithm | 18751 | 103 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 94 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 49896 | 79 | 1 |
| OTU after vsearch reclustering at 97% | 49896 | 47 | 1 |
| OTU vs after mumu cleaning algorithm | 49896 | 44 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 41 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 20133 | 57 | 1 |
| OTU after vsearch reclustering at 97% | 20133 | 33 | 1 |
| OTU vs after mumu cleaning algorithm | 20133 | 33 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 29 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 25167 | 60 | 1 |
| OTU after vsearch reclustering at 97% | 25167 | 52 | 1 |
| OTU vs after mumu cleaning algorithm | 25167 | 47 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 34 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 48782 | 104 | 1 |
| OTU after vsearch reclustering at 97% | 48782 | 65 | 1 |
| OTU vs after mumu cleaning algorithm | 48782 | 64 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 55 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 11338 | 114 | 1 |
| OTU after vsearch reclustering at 97% | 11338 | 106 | 1 |
| OTU vs after mumu cleaning algorithm | 11338 | 105 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 97 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 50126 | 66 | 1 |
| OTU after vsearch reclustering at 97% | 50126 | 39 | 1 |
| OTU vs after mumu cleaning algorithm | 50126 | 38 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 38 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 13661 | 113 | 1 |
| OTU after vsearch reclustering at 97% | 13661 | 105 | 1 |
| OTU vs after mumu cleaning algorithm | 13661 | 101 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 93 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 23233 | 104 | 1 |
| OTU after vsearch reclustering at 97% | 23233 | 90 | 1 |
| OTU vs after mumu cleaning algorithm | 23233 | 86 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 64 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 54651 | 62 | 1 |
| OTU after vsearch reclustering at 97% | 54651 | 25 | 1 |
| OTU vs after mumu cleaning algorithm | 54651 | 25 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 25 | 1 |
| nb_sequences | nb_clusters | nb_samples | |
|---|---|---|---|
| ASV denoising | 14493 | 77 | 1 |
| OTU after vsearch reclustering at 97% | 14493 | 62 | 1 |
| OTU vs after mumu cleaning algorithm | 14493 | 60 | 1 |
| OTU vs + mumu + rarefaction by sequencing depth | 2000 | 55 | 1 |
krona(clean_pq(d_pq, simplify_taxo = TRUE),
paste0(here::here("data/data_final/"), "krona_unite.html"),
name = "Unite"
)Cleaning suppress 2 taxa and 12 samples.
krona(clean_pq(d_pq, simplify_taxo = TRUE),
ranks = 8:14,
paste0(here::here("data/data_final/"), "krona_eukaryome.html"), name = "Eukaryome"
)Cleaning suppress 2 taxa and 12 samples.
merge_krona(c(
paste0(here::here("data/data_final/"), "krona_unite.html"),
paste0(here::here("data/data_final/"), "krona_eukaryome.html")
))krona(clean_pq(d_pq, simplify_taxo = TRUE),
paste0(here::here("data/data_final/"), "krona_unite_taxa.html"),
nb_seq = FALSE, name = "Unite"
)Cleaning suppress 2 taxa and 12 samples.
krona(clean_pq(d_pq, simplify_taxo = TRUE),
ranks = 8:14,
paste0(here::here("data/data_final/"), "krona_eukaryome_taxa.html"),
nb_seq = FALSE, name = "Eukaryome"
)Cleaning suppress 2 taxa and 12 samples.
merge_krona(
c(
paste0(here::here("data/data_final/"), "krona_unite_taxa.html"),
paste0(here::here("data/data_final/"), "krona_eukaryome_taxa.html")
),
output = paste0(here::here("data/data_final/"), "mergeKrona_taxa.html")
)tar_load(d_asv, store = here::here("_targets/"))
tar_load(d_vs, store = here::here("_targets/"))
tar_load(d_vs_mumu, store = here::here("_targets/"))
save(d_asv, d_vs, d_vs_mumu,
file = paste0(here::here("data/data_final/"), "phyloseq_object.Rdata")
)d_asv_Camila <- clean_pq(subset_samples(d_asv, Projet == "Camila"),
simplify_taxo = TRUE)Cleaning suppress 14510 taxa and 0 samples.
d_asv_DIVFUN <- clean_pq(subset_samples(d_asv, Projet == "DIVFUN"),
simplify_taxo = TRUE)Cleaning suppress 5742 taxa and 10 samples.
d_asv_Cistaceae <- clean_pq(subset_samples(d_asv, Projet == "Cistaceae"),
simplify_taxo = TRUE)Cleaning suppress 10821 taxa and 0 samples.
d_vs_Camila <- clean_pq(subset_samples(d_vs, Projet == "Camila"),
simplify_taxo = TRUE)Cleaning suppress 6286 taxa and 0 samples.
d_vs_DIVFUN <- clean_pq(subset_samples(d_vs, Projet == "DIVFUN"),
simplify_taxo = TRUE)Cleaning suppress 1643 taxa and 10 samples.
d_vs_Cistaceae <- clean_pq(subset_samples(d_vs, Projet == "Cistaceae"),
simplify_taxo = TRUE)Cleaning suppress 4631 taxa and 0 samples.
dir.create(paste0(here::here("data/data_final/"), "Camila"))Warning in dir.create(paste0(here::here("data/data_final/"), "Camila")):
'/home/adrien/Bureau/analyse_franck_camilla_jm_2024/bioinfo.starter/data/data_final/Camila'
existe déjà
dir.create(paste0(here::here("data/data_final/"), "DIVFUN"))Warning in dir.create(paste0(here::here("data/data_final/"), "DIVFUN")):
'/home/adrien/Bureau/analyse_franck_camilla_jm_2024/bioinfo.starter/data/data_final/DIVFUN'
existe déjà
dir.create(paste0(here::here("data/data_final/"), "Cistaceae"))Warning in dir.create(paste0(here::here("data/data_final/"), "Cistaceae")):
'/home/adrien/Bureau/analyse_franck_camilla_jm_2024/bioinfo.starter/data/data_final/Cistaceae'
existe déjà
save_pq(d_vs_Camila,
path = paste0(here::here("data/data_final/Camila/"),
"otu_reclustering_vsearch")
)Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(samp_1_S1, samp_10_S10, samp_11_S11, samp_12_S12,
samp_13_S13, samp_14_S14, samp_15_S15, samp_16_S16, samp_17_S17, samp_18_S18,
samp_19_S19, samp_2_S2, samp_20_S20, samp_21_S21, samp_22_S22, samp_23_S23,
samp_24_S24, samp_25_S25, samp_26_S26, samp_27_S27, samp_28_S28, samp_29_S29,
samp_3_S3, samp_30_S30, samp_31_S31, samp_32_S32, samp_33_S33, samp_34_S34,
samp_35_S35, samp_4_S4, samp_41_S38, samp_42_S39, samp_43_S40, samp_44_S41,
samp_45_S42, samp_46_S43, samp_47_S44, samp_48_S45, samp_49_S46, samp_5_S5,
samp_50_S47, samp_51_S48, samp_52_S49, samp_53_S50, samp_54_S51, samp_55_S52,
samp_56_S53, samp_57_S54, samp_58_S55, samp_59_S56, samp_6_S6, samp_60_S57,
samp_61_S58, samp_62_S59, samp_63_S60, samp_64_S61, samp_65_S62, samp_66_S63,
samp_67_S64, samp_69_S66, samp_7_S7, samp_70_S67, samp_71_S68, samp_72_S69,
samp_73_S70, samp_74_S71, samp_75_S72, samp_8_S8, samp_9_S9)`
Cleaning suppress 0 taxa and 0 samples.
save_pq(d_asv_Camila,
path = paste0(here::here("data/data_final/Camila/"),
"asv_dada2")
)Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(samp_1_S1, samp_10_S10, samp_11_S11, samp_12_S12, samp_13_S13, samp_14_S14, samp_15_S15, samp_16_S16, samp_17_S17, samp_18_S18, samp_19_S19, samp_2_S2, samp_20_S20, samp_21_S21, samp_22_S22, samp_23_S23, samp_24_S24, samp_25_S25, samp_26_S26, samp_27_S27, samp_28_S28, samp_29_S29, samp_3_S3, samp_30_S30, samp_31_S31, samp_32_S32, samp_33_S33, samp_34_S34, samp_35_S35, samp_4_S4, samp_41_S38, samp_42_S39, samp_43_S40, samp_44_S41, samp_45_S42, samp_46_S43, samp_47_S44, samp_48_S45, samp_49_S46, samp_5_S5, samp_50_S47, samp_51_S48, samp_52_S49, samp_53_S50, samp_54_S51, samp_55_S52, samp_56_S53, samp_57_S54, samp_58_S55, samp_59_S56, samp_6_S6, samp_60_S57, samp_61_S58, samp_62_S59, samp_63_S60, samp_64_S61, samp_65_S62, samp_66_S63, samp_67_S64, samp_69_S66, samp_7_S7, samp_70_S67, samp_71_S68, samp_72_S69, samp_73_S70, samp_74_S71, samp_75_S72, samp_8_S8, samp_9_S9)`Cleaning suppress 0 taxa and 0 samples.
save_pq(d_vs_DIVFUN,
path = paste0(here::here("data/data_final/DIVFUN/"),
"otu_reclustering_vsearch")
)Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(`samp_C-1-3-1_S236`, `samp_C-1-3-2_S237`, `samp_C-1-3-3_S238`, `samp_C-1-3-4_S239`, `samp_C1-1_S234`, `samp_C1-2_S235`, `samp_C2-1_S241`, `samp_C2-2-1_S242`, `samp_C2-2-2_S243`, `samp_C2-2-3_S244`, `samp_C2-2-5_S246`, `samp_C3-1_S248`, `samp_C4-1_S255`, `samp_C4-2-1_S256`, `samp_C4-2-2_S257`, `samp_C4-2-3_S258`, `samp_C4-2-4_S259`, `samp_C4-3_S261`, `samp_C5-1_S262`, `samp_C5-2-1_S263`, `samp_C5-2-2_S264`, `samp_C5-2-3_S265`, `samp_C5-2-4_S266`, `samp_C5-2-5_S267`, `samp_C5-3_S268`, `samp_C6-1-1_S269`, `samp_C6-1-2_S270`, `samp_C6-1-3_S271`, `samp_C6-1-4_S272`, `samp_C6-1-5_S273`, `samp_C6-2_S274`, samp_CT_S232, `samp_CT1-PL2_S128`, samp_DOM1_S368, samp_DOM2_S369, `samp_LVT1-1_S341`, `samp_LVT1-2-1_S342`, `samp_LVT1-2-2_S343`, `samp_LVT1-2-3_S344`, `samp_LVT1-2-4_S345`, `samp_LVT1-2-5_S346`, `samp_LVT1-3-1_S347`, `samp_LVT1-3-2_S348`, `samp_LVT1-3-3_S349`, `samp_LVT1-3-4_S350`, `samp_LVT1-3-5_S351`, `samp_LVT2-1_S352`, `samp_LVT2-2_S353`, `samp_LVT2-3-1_S354`, `samp_LVT2-3-2_S355`, `samp_LVT2-3-3_S356`, `samp_LVT2-3-4_S357`, `samp_LVT2-3-5_S358`, `samp_LVT3-1_S359`, `samp_LVT3-2_S360`, `samp_LVT3-3_S361`, `samp_LVT4-1_S362`, `samp_LVT4-2_S363`, `samp_LVT4-3_S364`, `samp_LVT5-1_S365`, `samp_LVT5-2_S366`, `samp_LVT5-3_S367`, `samp_PC1-1_S276`, `samp_PC1-2-1_S277`, `samp_PC1-2-2_S278`, `samp_PC1-2-3_S279`, `samp_PC1-2-4_S280`, `samp_PC1-2-5_S281`, `samp_PC1-3_S282`, `samp_PC2-1-1_S283`, `samp_PC2-1-2_S284`, `samp_PC2-1-3_S285`, `samp_PC2-1-4_S286`, `samp_PC2-1-5_S287`, `samp_PC2-2_S288`, `samp_PC2-3_S289`, `samp_PC3-1-1_S290`, `samp_PC3-1-2_S291`, `samp_PC3-1-3_S292`, `samp_PC3-1-5_S294`, `samp_PC3-2_S295`, `samp_PC3-3_S296`, `samp_PC4-1_S297`, `samp_PC4-2-2_S299`, `samp_PC4-2-3_S300`, `samp_PC4-2-5_S302`, `samp_PC4-3_S303`, `samp_PC5-1-1_S304`, `samp_PC5-1-2_S305`, `samp_PC5-1-3_S306`, `samp_PC5-1-4_S307`, `samp_PC5-1-5_S308`, `samp_PC5-2_S309`, `samp_PC5-3_S310`, `samp_PRL1-1-1_S311`, `samp_PRL1-1-2_S312`, `samp_PRL1-1-3_S313`, `samp_PRL1-1-4_S314`, `samp_PRL1-1-5_S315`, `samp_PRL1-2_S316`, `samp_PRL1-3_S317`, `samp_PRL2-1-1_S318`, `samp_PRL2-1-2_S319`, `samp_PRL2-1-3_S320`, `samp_PRL2-1-4_S321`, `samp_PRL2-1-5_S322`, `samp_PRL2-2_S323`, `samp_PRL2-3-1_S324`, `samp_PRL2-3-2_S325`, `samp_PRL2-3-3_S326`, `samp_PRL2-3-4_S327`, `samp_PRL2-3-5_S328`, `samp_PRL3-2_S330`, `samp_PRL3-3_S331`, `samp_PRL3-4_S332`, `samp_PRL4-1_S333`, `samp_PRL4-2_S334`, `samp_PRL4-3_S335`, `samp_PRL5-2_S336`, `samp_PRL5-3_S337`, `samp_PRL6-1_S338`, `samp_PRL6-2_S339`, `samp_PRL6-3_S340`)`Cleaning suppress 0 taxa and 0 samples.
save_pq(d_asv_DIVFUN,
path = paste0(here::here("data/data_final/DIVFUN/"),
"asv_dada2")
)Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(`samp_C-1-3-1_S236`, `samp_C-1-3-2_S237`, `samp_C-1-3-3_S238`, `samp_C-1-3-4_S239`, `samp_C1-1_S234`, `samp_C1-2_S235`, `samp_C2-1_S241`, `samp_C2-2-1_S242`, `samp_C2-2-2_S243`, `samp_C2-2-3_S244`, `samp_C2-2-5_S246`, `samp_C3-1_S248`, `samp_C4-1_S255`, `samp_C4-2-1_S256`, `samp_C4-2-2_S257`, `samp_C4-2-3_S258`, `samp_C4-2-4_S259`, `samp_C4-3_S261`, `samp_C5-1_S262`, `samp_C5-2-1_S263`, `samp_C5-2-2_S264`, `samp_C5-2-3_S265`, `samp_C5-2-4_S266`, `samp_C5-2-5_S267`, `samp_C5-3_S268`, `samp_C6-1-1_S269`, `samp_C6-1-2_S270`, `samp_C6-1-3_S271`, `samp_C6-1-4_S272`, `samp_C6-1-5_S273`, `samp_C6-2_S274`, samp_CT_S232, `samp_CT1-PL2_S128`, samp_DOM1_S368, samp_DOM2_S369, `samp_LVT1-1_S341`, `samp_LVT1-2-1_S342`, `samp_LVT1-2-2_S343`, `samp_LVT1-2-3_S344`, `samp_LVT1-2-4_S345`, `samp_LVT1-2-5_S346`, `samp_LVT1-3-1_S347`, `samp_LVT1-3-2_S348`, `samp_LVT1-3-3_S349`, `samp_LVT1-3-4_S350`, `samp_LVT1-3-5_S351`, `samp_LVT2-1_S352`, `samp_LVT2-2_S353`, `samp_LVT2-3-1_S354`, `samp_LVT2-3-2_S355`, `samp_LVT2-3-3_S356`, `samp_LVT2-3-4_S357`, `samp_LVT2-3-5_S358`, `samp_LVT3-1_S359`, `samp_LVT3-2_S360`, `samp_LVT3-3_S361`, `samp_LVT4-1_S362`, `samp_LVT4-2_S363`, `samp_LVT4-3_S364`, `samp_LVT5-1_S365`, `samp_LVT5-2_S366`, `samp_LVT5-3_S367`, `samp_PC1-1_S276`, `samp_PC1-2-1_S277`, `samp_PC1-2-2_S278`, `samp_PC1-2-3_S279`, `samp_PC1-2-4_S280`, `samp_PC1-2-5_S281`, `samp_PC1-3_S282`, `samp_PC2-1-1_S283`, `samp_PC2-1-2_S284`, `samp_PC2-1-3_S285`, `samp_PC2-1-4_S286`, `samp_PC2-1-5_S287`, `samp_PC2-2_S288`, `samp_PC2-3_S289`, `samp_PC3-1-1_S290`, `samp_PC3-1-2_S291`, `samp_PC3-1-3_S292`, `samp_PC3-1-5_S294`, `samp_PC3-2_S295`, `samp_PC3-3_S296`, `samp_PC4-1_S297`, `samp_PC4-2-2_S299`, `samp_PC4-2-3_S300`, `samp_PC4-2-5_S302`, `samp_PC4-3_S303`, `samp_PC5-1-1_S304`, `samp_PC5-1-2_S305`, `samp_PC5-1-3_S306`, `samp_PC5-1-4_S307`, `samp_PC5-1-5_S308`, `samp_PC5-2_S309`, `samp_PC5-3_S310`, `samp_PRL1-1-1_S311`, `samp_PRL1-1-2_S312`, `samp_PRL1-1-3_S313`, `samp_PRL1-1-4_S314`, `samp_PRL1-1-5_S315`, `samp_PRL1-2_S316`, `samp_PRL1-3_S317`, `samp_PRL2-1-1_S318`, `samp_PRL2-1-2_S319`, `samp_PRL2-1-3_S320`, `samp_PRL2-1-4_S321`, `samp_PRL2-1-5_S322`, `samp_PRL2-2_S323`, `samp_PRL2-3-1_S324`, `samp_PRL2-3-2_S325`, `samp_PRL2-3-3_S326`, `samp_PRL2-3-4_S327`, `samp_PRL2-3-5_S328`, `samp_PRL3-2_S330`, `samp_PRL3-3_S331`, `samp_PRL3-4_S332`, `samp_PRL4-1_S333`, `samp_PRL4-2_S334`, `samp_PRL4-3_S335`, `samp_PRL5-2_S336`, `samp_PRL5-3_S337`, `samp_PRL6-1_S338`, `samp_PRL6-2_S339`, `samp_PRL6-3_S340`)`Cleaning suppress 0 taxa and 0 samples.
save_pq(d_vs_Cistaceae,
path = paste0(here::here("data/data_final/Cistaceae/"),
"otu_reclustering_vsearch")
)Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(samp_F1Fe1_S196, `samp_F1Fe1-PL2_S125`, samp_F1Fe2_S197, `samp_F1Fe2-PL2_S133`, `samp_F1Fe2b-PL2_S157`, samp_F1Fe3_S198, `samp_F1Fe3-PL2_S141`, samp_F1Ft1_S199, `samp_F1Ft1b-PL2_S149`, samp_F1Ft2_S200, samp_F1Ft3_S201, `samp_F1Ft3-PL2_S165`, samp_F2Fe1_S202, `samp_F2Fe1-PL2_S78`, samp_F2Fe2_S203, `samp_F2Fe2-PL2_S86`, samp_F2Fe3_S204, `samp_F2Fe3-PL2_S94`, samp_F2Ft1_S205, `samp_F2Ft1b-PL2_S102`, samp_F2Ft2_S206, `samp_F2Ft2b-PL2_S110`, samp_F2Ft3_S207, `samp_F2Ft3b-PL2_S118`, samp_F3Fe1_S208, `samp_F3Fe1-PL2_S126`, samp_F3Fe2_S209, `samp_F3Fe2-PL2_S134`, `samp_F3Fe2b-PL2_S158`, samp_F3Fe3_S210, `samp_F3Fe3-PL2_S142`, samp_F3Ft1_S211, `samp_F3Ft1b-PL2_S150`, samp_F3Ft2_S212, samp_F3Ft3_S213, `samp_F3Ft3-PL2_S166`, samp_P1Fe1_S214, `samp_P1Fe1-PL2_S79`, samp_P1Fe2_S215, `samp_P1Fe2-PL2_S87`, samp_P1Fe3_S216, `samp_P1Fe3-PL2_S95`, samp_P1Ft1_S217, `samp_P1Ft1b-PL2_S103`, samp_P1Ft2_S218, `samp_P1Ft2b-PL2_S111`, `samp_P1Ft3b-PL2_S119`, samp_P2Fe1_S220, `samp_P2Fe1-PL2_S127`, samp_P2Fe2_S221, `samp_P2Fe2-PL2_S135`, `samp_P2Fe2b-PL2_S159`, samp_P2Fe3_S222, samp_P2Ft1_S223, `samp_P2Ft1b-PL2_S151`, samp_P2Ft2_S224, samp_P2Ft3_S225, `samp_P2Ft3-PL2_S167`, samp_P3Fe1_S226, `samp_P3Fe1-PL2_S80`, samp_P3Fe2_S227, `samp_P3Fe2-PL2_S88`, samp_P3Fe3_S228, `samp_P3Fe3-PL2_S96`, samp_P3Ft1_S229, `samp_P3Ft1b-PL2_S104`, samp_P3Ft2_S230, `samp_P3Ft2b-PL2_S112`, samp_P3Ft3_S231, `samp_P3Ft3b-PL2_S120`, samp_T1Fe1_S172, `samp_T1Fe1-PL2_S121`, `samp_t1Fe1b-PL2_S145`, samp_T1Fe2_S173, `samp_T1Fe2-PL2_S129`, `samp_T1Fe2b-PL2_S153`, samp_T1Fe3_S174, `samp_t1Fe3-PL2_S161`, `samp_T1Fe3-PL2a_S137`, samp_T1Ft1_S175, `samp_T1Ft1-PL2_S74`, `samp_t1Ft1b-PL2_S98`, samp_T1Ft2_S176, `samp_T1Ft2-PL2_S82`, `samp_t1Ft2b-PL2_S106`, samp_T1Ft3_S177, `samp_T1Ft3-PL2_S90`, `samp_t1Ft3b-PL2_S114`, samp_T1Ho1_S169, `samp_T1Ho1-PL2_S73`, `samp_t1Ho1b-PL2_S97`, samp_T1Ho2_S170, `samp_T1Ho2-PL2_S81`, `samp_t1Ho2b-PL2_S105`, samp_T1Ho3_S171, `samp_T1Ho3-PL2_S89`, `samp_t1Ho3b-PL2_S113`, samp_T2Fe1_S181, `samp_T2Fe1-PL2_S75`, `samp_t2Fe1b-PL2_S99`, samp_T2Fe2_S182, `samp_T2Fe2-PL2_S83`, `samp_t2Fe2b-PL2_S107`, samp_T2Fe3_S183, `samp_T2Fe3-PL2_S91`, `samp_t2Fe3b-PL2_S115`, samp_T2Ft1_S184, `samp_T2Ft1-PL2_S123`, `samp_t2Ft1b-PL2_S147`, samp_T2Ft2_S185, `samp_T2Ft2-PL2_S131`, `samp_T2Ft2b-PL2_S155`, samp_T2Ft3_S186, `samp_t2Ft3-PL2_S163`, `samp_T2Ft3-PL2a_S139`, samp_T2Ho1_S178, `samp_T2Ho1-PL2_S122`, `samp_t2Ho1b-PL2_S146`, samp_T2Ho2_S179, `samp_T2Ho2-PL2_S130`, `samp_T2Ho2b-PL2_S154`, samp_T2Ho3_S180, `samp_t2Ho3-PL2_S162`, `samp_T2Ho3-PL2a_S138`, samp_T3Fe1_S190, `samp_T3Fe1-PL2_S124`, `samp_t3Fe1b-PL2_S148`, samp_T3Fe2_S191, `samp_T3Fe2-PL2_S132`, `samp_T3Fe2b-PL2_S156`, samp_T3Fe3_S192, `samp_T3Fe3-PL2a_S140`, samp_T3Ft1_S193, `samp_T3Ft1-PL2_S77`, samp_T3Ft2_S194, `samp_T3Ft2-PL2_S85`, `samp_t3Ft2b-PL2_S109`, samp_T3Ft3_S195, `samp_T3Ft3-PL2_S93`, `samp_t3Ft3b-PL2_S117`, samp_T3Ho1_S187, `samp_T3Ho1-PL2_S76`, samp_T3Ho2_S188, `samp_T3Ho2-PL2_S84`, `samp_t3Ho2b-PL2_S108`, samp_T3Ho3_S189, `samp_T3Ho3-PL2_S92`)`Cleaning suppress 0 taxa and 0 samples.
save_pq(d_asv_Cistaceae,
path = paste0(here::here("data/data_final/Cistaceae/"),
"asv_dada2")
)Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(samp_F1Fe1_S196, `samp_F1Fe1-PL2_S125`, samp_F1Fe2_S197, `samp_F1Fe2-PL2_S133`, `samp_F1Fe2b-PL2_S157`, samp_F1Fe3_S198, `samp_F1Fe3-PL2_S141`, samp_F1Ft1_S199, `samp_F1Ft1b-PL2_S149`, samp_F1Ft2_S200, samp_F1Ft3_S201, `samp_F1Ft3-PL2_S165`, samp_F2Fe1_S202, `samp_F2Fe1-PL2_S78`, samp_F2Fe2_S203, `samp_F2Fe2-PL2_S86`, samp_F2Fe3_S204, `samp_F2Fe3-PL2_S94`, samp_F2Ft1_S205, `samp_F2Ft1b-PL2_S102`, samp_F2Ft2_S206, `samp_F2Ft2b-PL2_S110`, samp_F2Ft3_S207, `samp_F2Ft3b-PL2_S118`, samp_F3Fe1_S208, `samp_F3Fe1-PL2_S126`, samp_F3Fe2_S209, `samp_F3Fe2-PL2_S134`, `samp_F3Fe2b-PL2_S158`, samp_F3Fe3_S210, `samp_F3Fe3-PL2_S142`, samp_F3Ft1_S211, `samp_F3Ft1b-PL2_S150`, samp_F3Ft2_S212, samp_F3Ft3_S213, `samp_F3Ft3-PL2_S166`, samp_P1Fe1_S214, `samp_P1Fe1-PL2_S79`, samp_P1Fe2_S215, `samp_P1Fe2-PL2_S87`, samp_P1Fe3_S216, `samp_P1Fe3-PL2_S95`, samp_P1Ft1_S217, `samp_P1Ft1b-PL2_S103`, samp_P1Ft2_S218, `samp_P1Ft2b-PL2_S111`, `samp_P1Ft3b-PL2_S119`, samp_P2Fe1_S220, `samp_P2Fe1-PL2_S127`, samp_P2Fe2_S221, `samp_P2Fe2-PL2_S135`, `samp_P2Fe2b-PL2_S159`, samp_P2Fe3_S222, samp_P2Ft1_S223, `samp_P2Ft1b-PL2_S151`, samp_P2Ft2_S224, samp_P2Ft3_S225, `samp_P2Ft3-PL2_S167`, samp_P3Fe1_S226, `samp_P3Fe1-PL2_S80`, samp_P3Fe2_S227, `samp_P3Fe2-PL2_S88`, samp_P3Fe3_S228, `samp_P3Fe3-PL2_S96`, samp_P3Ft1_S229, `samp_P3Ft1b-PL2_S104`, samp_P3Ft2_S230, `samp_P3Ft2b-PL2_S112`, samp_P3Ft3_S231, `samp_P3Ft3b-PL2_S120`, samp_T1Fe1_S172, `samp_T1Fe1-PL2_S121`, `samp_t1Fe1b-PL2_S145`, samp_T1Fe2_S173, `samp_T1Fe2-PL2_S129`, `samp_T1Fe2b-PL2_S153`, samp_T1Fe3_S174, `samp_t1Fe3-PL2_S161`, `samp_T1Fe3-PL2a_S137`, samp_T1Ft1_S175, `samp_T1Ft1-PL2_S74`, `samp_t1Ft1b-PL2_S98`, samp_T1Ft2_S176, `samp_T1Ft2-PL2_S82`, `samp_t1Ft2b-PL2_S106`, samp_T1Ft3_S177, `samp_T1Ft3-PL2_S90`, `samp_t1Ft3b-PL2_S114`, samp_T1Ho1_S169, `samp_T1Ho1-PL2_S73`, `samp_t1Ho1b-PL2_S97`, samp_T1Ho2_S170, `samp_T1Ho2-PL2_S81`, `samp_t1Ho2b-PL2_S105`, samp_T1Ho3_S171, `samp_T1Ho3-PL2_S89`, `samp_t1Ho3b-PL2_S113`, samp_T2Fe1_S181, `samp_T2Fe1-PL2_S75`, `samp_t2Fe1b-PL2_S99`, samp_T2Fe2_S182, `samp_T2Fe2-PL2_S83`, `samp_t2Fe2b-PL2_S107`, samp_T2Fe3_S183, `samp_T2Fe3-PL2_S91`, `samp_t2Fe3b-PL2_S115`, samp_T2Ft1_S184, `samp_T2Ft1-PL2_S123`, `samp_t2Ft1b-PL2_S147`, samp_T2Ft2_S185, `samp_T2Ft2-PL2_S131`, `samp_T2Ft2b-PL2_S155`, samp_T2Ft3_S186, `samp_t2Ft3-PL2_S163`, `samp_T2Ft3-PL2a_S139`, samp_T2Ho1_S178, `samp_T2Ho1-PL2_S122`, `samp_t2Ho1b-PL2_S146`, samp_T2Ho2_S179, `samp_T2Ho2-PL2_S130`, `samp_T2Ho2b-PL2_S154`, samp_T2Ho3_S180, `samp_t2Ho3-PL2_S162`, `samp_T2Ho3-PL2a_S138`, samp_T3Fe1_S190, `samp_T3Fe1-PL2_S124`, `samp_t3Fe1b-PL2_S148`, samp_T3Fe2_S191, `samp_T3Fe2-PL2_S132`, `samp_T3Fe2b-PL2_S156`, samp_T3Fe3_S192, `samp_T3Fe3-PL2a_S140`, samp_T3Ft1_S193, `samp_T3Ft1-PL2_S77`, samp_T3Ft2_S194, `samp_T3Ft2-PL2_S85`, `samp_t3Ft2b-PL2_S109`, samp_T3Ft3_S195, `samp_T3Ft3-PL2_S93`, `samp_t3Ft3b-PL2_S117`, samp_T3Ho1_S187, `samp_T3Ho1-PL2_S76`, samp_T3Ho2_S188, `samp_T3Ho2-PL2_S84`, `samp_t3Ho2b-PL2_S108`, samp_T3Ho3_S189, `samp_T3Ho3-PL2_S92`)`Cleaning suppress 0 taxa and 0 samples.
path_camila <- here::here("data/data_final/Camila/")
krona(d_vs_Camila,
paste0(path_camila, "krona_unite_nb_seq.html"),
name = "Nb_seq_Unite",
ranks=c(1:7)
)
krona(d_vs_Camila,
nb_seq = FALSE,
paste0(path_camila, "krona_unite_nb_asv.html"),
name = "Nb_ASV_Unite",
ranks=c(1:7)
)
krona(d_vs_Camila,
paste0(path_camila, "krona_eukaryome_nb_seq.html"),
name = "Nb_seq_Euk",
ranks=c(8:14)
)
krona(d_vs_Camila,
nb_seq = FALSE,
paste0(path_camila, "krona_eukaryome_nb_asv.html"),
name = "Nb_ASV_Euk",
ranks=c(8:14)
)
merge_krona(
c(
paste0(path_camila, "krona_unite_nb_asv.html"),
paste0(path_camila, "krona_eukaryome_nb_asv.html"),
paste0(path_camila, "krona_unite_nb_seq.html"),
paste0(path_camila, "krona_eukaryome_nb_seq.html")
),
output = paste0(path_camila, "krona_unite_eukaryome.html")
)
unlink(paste0(path_camila, "krona_unite_nb_asv.html"))
unlink(paste0(path_camila, "krona_unite_nb_seq.html"))
unlink(paste0(path_camila, "krona_eukaryome_nb_asv.html"))
unlink(paste0(path_camila, "krona_eukaryome_nb_seq.html"))path_divfun <- here::here("data/data_final/DIVFUN/")
krona(d_vs_DIVFUN,
paste0(path_divfun, "krona_unite_nb_seq.html"),
name = "Nb_seq_Unite",
ranks=c(1:7)
)
krona(d_vs_DIVFUN,
nb_seq = FALSE,
paste0(path_divfun, "krona_unite_nb_asv.html"),
name = "Nb_ASV_Unite",
ranks=c(1:7)
)
krona(d_vs_DIVFUN,
paste0(path_divfun, "krona_eukaryome_nb_seq.html"),
name = "Nb_seq_Euk",
ranks=c(8:14)
)
krona(d_vs_DIVFUN,
nb_seq = FALSE,
paste0(path_divfun, "krona_eukaryome_nb_asv.html"),
name = "Nb_ASV_Euk",
ranks=c(8:14)
)
merge_krona(
c(
paste0(path_divfun, "krona_unite_nb_asv.html"),
paste0(path_divfun, "krona_eukaryome_nb_asv.html"),
paste0(path_divfun, "krona_unite_nb_seq.html"),
paste0(path_divfun, "krona_eukaryome_nb_seq.html")
),
output = paste0(path_divfun, "krona_unite_eukaryome.html")
)
unlink(paste0(path_divfun, "krona_unite_nb_asv.html"))
unlink(paste0(path_divfun, "krona_unite_nb_seq.html"))
unlink(paste0(path_divfun, "krona_eukaryome_nb_asv.html"))
unlink(paste0(path_divfun, "krona_eukaryome_nb_seq.html"))path_cistaceae <- here::here("data/data_final/Cistaceae/")
krona(d_vs_Cistaceae,
paste0(path_cistaceae, "krona_unite_nb_seq.html"),
name = "Nb_seq_Unite",
ranks=c(1:7)
)
krona(d_vs_Cistaceae,
nb_seq = FALSE,
paste0(path_cistaceae, "krona_unite_nb_asv.html"),
name = "Nb_ASV_Unite",
ranks=c(1:7)
)
krona(d_vs_Cistaceae,
paste0(path_cistaceae, "krona_eukaryome_nb_seq.html"),
name = "Nb_seq_Euk",
ranks=c(8:14)
)
krona(d_vs_Cistaceae,
nb_seq = FALSE,
paste0(path_cistaceae, "krona_eukaryome_nb_asv.html"),
name = "Nb_ASV_Euk",
ranks=c(8:14)
)
merge_krona(
c(
paste0(path_cistaceae, "krona_unite_nb_asv.html"),
paste0(path_cistaceae, "krona_eukaryome_nb_asv.html"),
paste0(path_cistaceae, "krona_unite_nb_seq.html"),
paste0(path_cistaceae, "krona_eukaryome_nb_seq.html")
),
output = paste0(path_cistaceae, "krona_unite_eukaryome.html")
)
unlink(paste0(path_cistaceae, "krona_unite_nb_asv.html"))
unlink(paste0(path_cistaceae, "krona_unite_nb_seq.html"))
unlink(paste0(path_cistaceae, "krona_eukaryome_nb_asv.html"))
unlink(paste0(path_cistaceae, "krona_eukaryome_nb_seq.html"))krona(subset_taxa(d_asv, Genus_Eukaryome=="Apiotrichum"),
ranks=c(1:7),
nb_seq= FALSE,
file = paste0(here::here("data/data_final/"),
"Apiotrichum_fromEUK_uniteTax.html")
)Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data/data_final/information_run.txt .
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] emojifont_0.5.5 patchwork_1.3.0 MiscMetabar_0.10.1 purrr_1.0.2
[5] dplyr_1.1.4 dada2_1.34.0 Rcpp_1.0.13-1 ggplot2_3.5.1
[9] phyloseq_1.50.0 targets_1.9.0 knitr_1.49
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1
[3] jsonlite_1.8.9 magrittr_2.0.3
[5] farver_2.1.2 rmarkdown_2.29
[7] zlibbioc_1.52.0 vctrs_0.6.5
[9] multtest_2.62.0 memoise_2.0.1
[11] Rsamtools_2.22.0 benchmarkme_1.0.8
[13] htmltools_0.5.8.1 S4Arrays_1.6.0
[15] Rhdf5lib_1.28.0 SparseArray_1.6.0
[17] rhdf5_2.50.0 sass_0.4.9
[19] bslib_0.8.0 htmlwidgets_1.6.4
[21] plyr_1.8.9 cachem_1.1.0
[23] conflicted_1.2.0 GenomicAlignments_1.42.0
[25] igraph_2.1.1 lifecycle_1.0.4
[27] iterators_1.0.14 pkgconfig_2.0.3
[29] Matrix_1.7-1 R6_2.5.1
[31] fastmap_1.2.0 GenomeInfoDbData_1.2.13
[33] MatrixGenerics_1.18.0 digest_0.6.37
[35] showtext_0.9-7 colorspace_2.1-1
[37] ShortRead_1.64.0 S4Vectors_0.44.0
[39] ps_1.8.1 rprojroot_2.0.4
[41] crosstalk_1.2.1 GenomicRanges_1.58.0
[43] base64url_1.4 hwriter_1.3.2.1
[45] vegan_2.6-8 labeling_0.4.3
[47] fansi_1.0.6 httr_1.4.7
[49] abind_1.4-8 mgcv_1.9-1
[51] compiler_4.4.2 here_1.0.1
[53] withr_3.0.2 doParallel_1.0.17
[55] backports_1.5.0 BiocParallel_1.40.0
[57] MASS_7.3-61 DelayedArray_0.32.0
[59] biomformat_1.34.0 permute_0.9-7
[61] tools_4.4.2 ape_5.8
[63] glue_1.8.0 callr_3.7.6
[65] nlme_3.1-166 rhdf5filters_1.18.0
[67] grid_4.4.2 cluster_2.1.6
[69] reshape2_1.4.4 ade4_1.7-22
[71] generics_0.1.3 gtable_0.3.6
[73] data.table_1.16.2 utf8_1.2.4
[75] XVector_0.46.0 BiocGenerics_0.52.0
[77] foreach_1.5.2 pillar_1.9.0
[79] stringr_1.5.1 benchmarkmeData_1.0.4
[81] splines_4.4.2 lattice_0.22-6
[83] showtextdb_3.0 renv_1.0.11
[85] survival_3.7-0 deldir_2.0-4
[87] tidyselect_1.2.1 Biostrings_2.74.0
[89] IRanges_2.40.0 SummarizedExperiment_1.36.0
[91] stats4_4.4.2 xfun_0.49
[93] Biobase_2.66.0 matrixStats_1.4.1
[95] DT_0.33 visNetwork_2.1.2
[97] proto_1.0.0 stringi_1.8.4
[99] UCSC.utils_1.2.0 yaml_2.3.10
[101] evaluate_1.0.1 codetools_0.2-20
[103] interp_1.1-6 tibble_3.2.1
[105] autometric_0.1.2 BiocManager_1.30.25
[107] cli_3.6.3 RcppParallel_5.1.9
[109] secretbase_1.0.3 jquerylib_0.1.4
[111] munsell_0.5.1 processx_3.8.4
[113] GenomeInfoDb_1.42.0 greenAlgoR_0.1.1
[115] png_0.1-8 parallel_4.4.2
[117] latticeExtra_0.6-30 jpeg_0.1-10
[119] bitops_1.0-9 pwalign_1.2.0
[121] viridisLite_0.4.2 scales_1.3.0
[123] sysfonts_0.8.9 crayon_1.5.3
[125] rlang_1.1.4
@online{taudière2024,
author = {Taudière, Adrien},
title = {Bioinformatics Pipeline Summary},
date = {2024-12-03},
langid = {en}
}